Starting phenix.real_space_refine on Thu Mar 5 05:49:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6l7a_0841/03_2026/6l7a_0841.cif Found real_map, /net/cci-nas-00/data/ceres_data/6l7a_0841/03_2026/6l7a_0841.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6l7a_0841/03_2026/6l7a_0841.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6l7a_0841/03_2026/6l7a_0841.map" model { file = "/net/cci-nas-00/data/ceres_data/6l7a_0841/03_2026/6l7a_0841.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6l7a_0841/03_2026/6l7a_0841.cif" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 12438 2.51 5 N 3411 2.21 5 O 3780 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 126 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19701 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1914 Classifications: {'peptide': 246} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 233} Chain breaks: 1 Chain: "J" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 275 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 3, 'TRANS': 32} Restraints were copied for chains: B, C, D, E, F, G, H, I, K, L, M, N, O, P, Q, R Time building chain proxies: 2.05, per 1000 atoms: 0.10 Number of scatterers: 19701 At special positions: 0 Unit cell: (134.64, 133.32, 121.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 3780 8.00 N 3411 7.00 C 12438 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 841.2 milliseconds 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4680 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 27 sheets defined 33.0% alpha, 136.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 18 through 26 removed outlier: 4.007A pdb=" N LYS A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N HIS A 26 " --> pdb=" O LYS A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 74 removed outlier: 3.537A pdb=" N MET A 67 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL A 69 " --> pdb=" O THR A 65 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR A 70 " --> pdb=" O ALA A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 102 removed outlier: 3.678A pdb=" N ILE A 95 " --> pdb=" O ASN A 91 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU A 101 " --> pdb=" O ARG A 97 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 234 removed outlier: 3.705A pdb=" N MET A 217 " --> pdb=" O MET A 213 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE A 225 " --> pdb=" O GLU A 221 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE A 232 " --> pdb=" O ILE A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 246 removed outlier: 3.825A pdb=" N GLN A 246 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 256 removed outlier: 3.788A pdb=" N HIS A 255 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 26 removed outlier: 4.007A pdb=" N LYS B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N HIS B 26 " --> pdb=" O LYS B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 74 removed outlier: 3.537A pdb=" N MET B 67 " --> pdb=" O SER B 63 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL B 69 " --> pdb=" O THR B 65 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR B 70 " --> pdb=" O ALA B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 102 removed outlier: 3.678A pdb=" N ILE B 95 " --> pdb=" O ASN B 91 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU B 101 " --> pdb=" O ARG B 97 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 234 removed outlier: 3.704A pdb=" N MET B 217 " --> pdb=" O MET B 213 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE B 225 " --> pdb=" O GLU B 221 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B 232 " --> pdb=" O ILE B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 246 removed outlier: 3.825A pdb=" N GLN B 246 " --> pdb=" O ALA B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 256 removed outlier: 3.789A pdb=" N HIS B 255 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET B 256 " --> pdb=" O LYS B 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 26 removed outlier: 4.006A pdb=" N LYS C 22 " --> pdb=" O ALA C 18 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N HIS C 26 " --> pdb=" O LYS C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 74 removed outlier: 3.536A pdb=" N MET C 67 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL C 69 " --> pdb=" O THR C 65 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR C 70 " --> pdb=" O ALA C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 102 removed outlier: 3.678A pdb=" N ILE C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU C 101 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN C 102 " --> pdb=" O ALA C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 234 removed outlier: 3.705A pdb=" N MET C 217 " --> pdb=" O MET C 213 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR C 222 " --> pdb=" O SER C 218 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE C 225 " --> pdb=" O GLU C 221 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE C 232 " --> pdb=" O ILE C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 246 removed outlier: 3.825A pdb=" N GLN C 246 " --> pdb=" O ALA C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 256 removed outlier: 3.788A pdb=" N HIS C 255 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET C 256 " --> pdb=" O LYS C 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 26 removed outlier: 4.007A pdb=" N LYS D 22 " --> pdb=" O ALA D 18 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N HIS D 26 " --> pdb=" O LYS D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 74 removed outlier: 3.535A pdb=" N MET D 67 " --> pdb=" O SER D 63 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL D 69 " --> pdb=" O THR D 65 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR D 70 " --> pdb=" O ALA D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 102 removed outlier: 3.678A pdb=" N ILE D 95 " --> pdb=" O ASN D 91 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU D 101 " --> pdb=" O ARG D 97 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN D 102 " --> pdb=" O ALA D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 234 removed outlier: 3.705A pdb=" N MET D 217 " --> pdb=" O MET D 213 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE D 225 " --> pdb=" O GLU D 221 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE D 232 " --> pdb=" O ILE D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 246 removed outlier: 3.826A pdb=" N GLN D 246 " --> pdb=" O ALA D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 256 removed outlier: 3.788A pdb=" N HIS D 255 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET D 256 " --> pdb=" O LYS D 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 26 removed outlier: 4.006A pdb=" N LYS E 22 " --> pdb=" O ALA E 18 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N HIS E 26 " --> pdb=" O LYS E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 74 removed outlier: 3.537A pdb=" N MET E 67 " --> pdb=" O SER E 63 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL E 69 " --> pdb=" O THR E 65 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR E 70 " --> pdb=" O ALA E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 102 removed outlier: 3.678A pdb=" N ILE E 95 " --> pdb=" O ASN E 91 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU E 101 " --> pdb=" O ARG E 97 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 234 removed outlier: 3.705A pdb=" N MET E 217 " --> pdb=" O MET E 213 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE E 225 " --> pdb=" O GLU E 221 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE E 232 " --> pdb=" O ILE E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 246 removed outlier: 3.826A pdb=" N GLN E 246 " --> pdb=" O ALA E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 256 removed outlier: 3.788A pdb=" N HIS E 255 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET E 256 " --> pdb=" O LYS E 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 26 removed outlier: 4.007A pdb=" N LYS F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N HIS F 26 " --> pdb=" O LYS F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 74 removed outlier: 3.537A pdb=" N MET F 67 " --> pdb=" O SER F 63 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL F 69 " --> pdb=" O THR F 65 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR F 70 " --> pdb=" O ALA F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 102 removed outlier: 3.677A pdb=" N ILE F 95 " --> pdb=" O ASN F 91 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU F 101 " --> pdb=" O ARG F 97 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN F 102 " --> pdb=" O ALA F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 234 removed outlier: 3.705A pdb=" N MET F 217 " --> pdb=" O MET F 213 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR F 222 " --> pdb=" O SER F 218 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE F 225 " --> pdb=" O GLU F 221 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE F 232 " --> pdb=" O ILE F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 246 removed outlier: 3.826A pdb=" N GLN F 246 " --> pdb=" O ALA F 243 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 256 removed outlier: 3.788A pdb=" N HIS F 255 " --> pdb=" O VAL F 251 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET F 256 " --> pdb=" O LYS F 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 26 removed outlier: 4.007A pdb=" N LYS G 22 " --> pdb=" O ALA G 18 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N HIS G 26 " --> pdb=" O LYS G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 74 removed outlier: 3.536A pdb=" N MET G 67 " --> pdb=" O SER G 63 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL G 69 " --> pdb=" O THR G 65 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR G 70 " --> pdb=" O ALA G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 102 removed outlier: 3.678A pdb=" N ILE G 95 " --> pdb=" O ASN G 91 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU G 101 " --> pdb=" O ARG G 97 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN G 102 " --> pdb=" O ALA G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 234 removed outlier: 3.705A pdb=" N MET G 217 " --> pdb=" O MET G 213 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR G 222 " --> pdb=" O SER G 218 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE G 225 " --> pdb=" O GLU G 221 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE G 232 " --> pdb=" O ILE G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 241 through 246 removed outlier: 3.825A pdb=" N GLN G 246 " --> pdb=" O ALA G 243 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 256 removed outlier: 3.787A pdb=" N HIS G 255 " --> pdb=" O VAL G 251 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET G 256 " --> pdb=" O LYS G 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 26 removed outlier: 4.007A pdb=" N LYS H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N HIS H 26 " --> pdb=" O LYS H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 74 removed outlier: 3.536A pdb=" N MET H 67 " --> pdb=" O SER H 63 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL H 69 " --> pdb=" O THR H 65 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR H 70 " --> pdb=" O ALA H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 102 removed outlier: 3.678A pdb=" N ILE H 95 " --> pdb=" O ASN H 91 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU H 101 " --> pdb=" O ARG H 97 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN H 102 " --> pdb=" O ALA H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 234 removed outlier: 3.705A pdb=" N MET H 217 " --> pdb=" O MET H 213 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR H 222 " --> pdb=" O SER H 218 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE H 225 " --> pdb=" O GLU H 221 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE H 232 " --> pdb=" O ILE H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 241 through 246 removed outlier: 3.825A pdb=" N GLN H 246 " --> pdb=" O ALA H 243 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 256 removed outlier: 3.788A pdb=" N HIS H 255 " --> pdb=" O VAL H 251 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET H 256 " --> pdb=" O LYS H 252 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 26 removed outlier: 4.007A pdb=" N LYS I 22 " --> pdb=" O ALA I 18 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N HIS I 26 " --> pdb=" O LYS I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 74 removed outlier: 3.536A pdb=" N MET I 67 " --> pdb=" O SER I 63 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL I 69 " --> pdb=" O THR I 65 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR I 70 " --> pdb=" O ALA I 66 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 102 removed outlier: 3.678A pdb=" N ILE I 95 " --> pdb=" O ASN I 91 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU I 101 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN I 102 " --> pdb=" O ALA I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 211 through 234 removed outlier: 3.704A pdb=" N MET I 217 " --> pdb=" O MET I 213 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR I 222 " --> pdb=" O SER I 218 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE I 225 " --> pdb=" O GLU I 221 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE I 232 " --> pdb=" O ILE I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 241 through 246 removed outlier: 3.826A pdb=" N GLN I 246 " --> pdb=" O ALA I 243 " (cutoff:3.500A) Processing helix chain 'I' and resid 247 through 256 removed outlier: 3.788A pdb=" N HIS I 255 " --> pdb=" O VAL I 251 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET I 256 " --> pdb=" O LYS I 252 " (cutoff:3.500A) Processing helix chain 'J' and resid 15 through 17 No H-bonds generated for 'chain 'J' and resid 15 through 17' Processing helix chain 'J' and resid 18 through 28 removed outlier: 3.519A pdb=" N ASN J 24 " --> pdb=" O ALA J 20 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA J 26 " --> pdb=" O LEU J 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 15 through 17 No H-bonds generated for 'chain 'K' and resid 15 through 17' Processing helix chain 'K' and resid 18 through 28 removed outlier: 3.519A pdb=" N ASN K 24 " --> pdb=" O ALA K 20 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA K 26 " --> pdb=" O LEU K 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 15 through 17 No H-bonds generated for 'chain 'L' and resid 15 through 17' Processing helix chain 'L' and resid 18 through 28 removed outlier: 3.520A pdb=" N ASN L 24 " --> pdb=" O ALA L 20 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA L 26 " --> pdb=" O LEU L 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 17 No H-bonds generated for 'chain 'M' and resid 15 through 17' Processing helix chain 'M' and resid 18 through 28 removed outlier: 3.520A pdb=" N ASN M 24 " --> pdb=" O ALA M 20 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA M 26 " --> pdb=" O LEU M 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 15 through 17 No H-bonds generated for 'chain 'N' and resid 15 through 17' Processing helix chain 'N' and resid 18 through 28 removed outlier: 3.520A pdb=" N ASN N 24 " --> pdb=" O ALA N 20 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA N 26 " --> pdb=" O LEU N 22 " (cutoff:3.500A) Processing helix chain 'O' and resid 15 through 17 No H-bonds generated for 'chain 'O' and resid 15 through 17' Processing helix chain 'O' and resid 18 through 28 removed outlier: 3.519A pdb=" N ASN O 24 " --> pdb=" O ALA O 20 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA O 26 " --> pdb=" O LEU O 22 " (cutoff:3.500A) Processing helix chain 'P' and resid 15 through 17 No H-bonds generated for 'chain 'P' and resid 15 through 17' Processing helix chain 'P' and resid 18 through 28 removed outlier: 3.520A pdb=" N ASN P 24 " --> pdb=" O ALA P 20 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA P 26 " --> pdb=" O LEU P 22 " (cutoff:3.500A) Processing helix chain 'Q' and resid 15 through 17 No H-bonds generated for 'chain 'Q' and resid 15 through 17' Processing helix chain 'Q' and resid 18 through 28 removed outlier: 3.519A pdb=" N ASN Q 24 " --> pdb=" O ALA Q 20 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA Q 26 " --> pdb=" O LEU Q 22 " (cutoff:3.500A) Processing helix chain 'R' and resid 15 through 17 No H-bonds generated for 'chain 'R' and resid 15 through 17' Processing helix chain 'R' and resid 18 through 28 removed outlier: 3.519A pdb=" N ASN R 24 " --> pdb=" O ALA R 20 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA R 26 " --> pdb=" O LEU R 22 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 14 removed outlier: 5.867A pdb=" N ILE I 171 " --> pdb=" O ASN I 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN I 165 " --> pdb=" O ILE I 171 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER I 173 " --> pdb=" O VAL I 163 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE I 146 " --> pdb=" O ALA I 141 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA I 141 " --> pdb=" O ILE I 146 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA I 148 " --> pdb=" O VAL I 139 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL I 139 " --> pdb=" O ALA I 148 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N THR I 150 " --> pdb=" O GLY I 137 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY I 137 " --> pdb=" O THR I 150 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR I 152 " --> pdb=" O LYS I 135 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS I 135 " --> pdb=" O TYR I 152 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU I 154 " --> pdb=" O ASN I 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN I 133 " --> pdb=" O LEU I 154 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL I 134 " --> pdb=" O ASN A 209 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER I 136 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR A 207 " --> pdb=" O SER I 136 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL A 204 " --> pdb=" O ALA A 188 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ILE A 171 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN A 165 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER A 173 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE A 146 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA A 141 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA A 148 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL A 139 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR A 150 " --> pdb=" O GLY A 137 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY A 137 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR A 152 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS A 135 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU A 154 " --> pdb=" O ASN A 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN A 133 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL A 134 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A 136 " --> pdb=" O THR B 207 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR B 207 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL B 204 " --> pdb=" O ALA B 188 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ILE B 171 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN B 165 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER B 173 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE B 146 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA B 141 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ALA B 148 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL B 139 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR B 150 " --> pdb=" O GLY B 137 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY B 137 " --> pdb=" O THR B 150 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR B 152 " --> pdb=" O LYS B 135 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS B 135 " --> pdb=" O TYR B 152 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU B 154 " --> pdb=" O ASN B 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN B 133 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL B 134 " --> pdb=" O ASN C 209 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER B 136 " --> pdb=" O THR C 207 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR C 207 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL C 204 " --> pdb=" O ALA C 188 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ILE C 171 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN C 165 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER C 173 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE C 146 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA C 141 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ALA C 148 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL C 139 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR C 150 " --> pdb=" O GLY C 137 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY C 137 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR C 152 " --> pdb=" O LYS C 135 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS C 135 " --> pdb=" O TYR C 152 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU C 154 " --> pdb=" O ASN C 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN C 133 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL C 134 " --> pdb=" O ASN D 209 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER C 136 " --> pdb=" O THR D 207 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR D 207 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL D 204 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ILE D 171 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN D 165 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER D 173 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE D 146 " --> pdb=" O ALA D 141 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA D 141 " --> pdb=" O ILE D 146 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA D 148 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL D 139 " --> pdb=" O ALA D 148 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR D 150 " --> pdb=" O GLY D 137 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLY D 137 " --> pdb=" O THR D 150 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR D 152 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS D 135 " --> pdb=" O TYR D 152 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU D 154 " --> pdb=" O ASN D 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN D 133 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL D 134 " --> pdb=" O ASN E 209 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER D 136 " --> pdb=" O THR E 207 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR E 207 " --> pdb=" O SER D 136 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL E 204 " --> pdb=" O ALA E 188 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ILE E 171 " --> pdb=" O ASN E 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN E 165 " --> pdb=" O ILE E 171 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER E 173 " --> pdb=" O VAL E 163 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE E 146 " --> pdb=" O ALA E 141 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA E 141 " --> pdb=" O ILE E 146 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ALA E 148 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL E 139 " --> pdb=" O ALA E 148 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR E 150 " --> pdb=" O GLY E 137 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLY E 137 " --> pdb=" O THR E 150 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR E 152 " --> pdb=" O LYS E 135 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LYS E 135 " --> pdb=" O TYR E 152 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU E 154 " --> pdb=" O ASN E 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN E 133 " --> pdb=" O LEU E 154 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL E 134 " --> pdb=" O ASN F 209 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER E 136 " --> pdb=" O THR F 207 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR F 207 " --> pdb=" O SER E 136 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL F 204 " --> pdb=" O ALA F 188 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ILE F 171 " --> pdb=" O ASN F 165 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ASN F 165 " --> pdb=" O ILE F 171 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER F 173 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE F 146 " --> pdb=" O ALA F 141 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA F 141 " --> pdb=" O ILE F 146 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA F 148 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL F 139 " --> pdb=" O ALA F 148 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR F 150 " --> pdb=" O GLY F 137 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY F 137 " --> pdb=" O THR F 150 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR F 152 " --> pdb=" O LYS F 135 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS F 135 " --> pdb=" O TYR F 152 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU F 154 " --> pdb=" O ASN F 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN F 133 " --> pdb=" O LEU F 154 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL F 134 " --> pdb=" O ASN G 209 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER F 136 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N THR G 207 " --> pdb=" O SER F 136 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL G 204 " --> pdb=" O ALA G 188 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ILE G 171 " --> pdb=" O ASN G 165 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ASN G 165 " --> pdb=" O ILE G 171 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER G 173 " --> pdb=" O VAL G 163 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE G 146 " --> pdb=" O ALA G 141 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA G 141 " --> pdb=" O ILE G 146 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA G 148 " --> pdb=" O VAL G 139 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL G 139 " --> pdb=" O ALA G 148 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR G 150 " --> pdb=" O GLY G 137 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLY G 137 " --> pdb=" O THR G 150 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR G 152 " --> pdb=" O LYS G 135 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS G 135 " --> pdb=" O TYR G 152 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU G 154 " --> pdb=" O ASN G 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN G 133 " --> pdb=" O LEU G 154 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N VAL G 134 " --> pdb=" O ASN H 209 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR H 207 " --> pdb=" O SER G 136 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL H 204 " --> pdb=" O ALA H 188 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ILE H 171 " --> pdb=" O ASN H 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN H 165 " --> pdb=" O ILE H 171 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER H 173 " --> pdb=" O VAL H 163 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN H 42 " --> pdb=" O GLY H 125 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 13 through 14 removed outlier: 4.039A pdb=" N VAL I 204 " --> pdb=" O ALA I 188 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR I 207 " --> pdb=" O SER H 136 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER H 136 " --> pdb=" O THR I 207 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL H 134 " --> pdb=" O ASN I 209 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN H 133 " --> pdb=" O LEU H 154 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU H 154 " --> pdb=" O ASN H 133 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS H 135 " --> pdb=" O TYR H 152 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR H 152 " --> pdb=" O LYS H 135 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY H 137 " --> pdb=" O THR H 150 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR H 150 " --> pdb=" O GLY H 137 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL H 139 " --> pdb=" O ALA H 148 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA H 148 " --> pdb=" O VAL H 139 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA H 141 " --> pdb=" O ILE H 146 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE H 146 " --> pdb=" O ALA H 141 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN H 42 " --> pdb=" O GLY H 125 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 13 through 14 removed outlier: 5.867A pdb=" N ILE I 171 " --> pdb=" O ASN I 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN I 165 " --> pdb=" O ILE I 171 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER I 173 " --> pdb=" O VAL I 163 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN I 42 " --> pdb=" O GLY I 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 13 through 14 removed outlier: 5.867A pdb=" N ILE I 171 " --> pdb=" O ASN I 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN I 165 " --> pdb=" O ILE I 171 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER I 173 " --> pdb=" O VAL I 163 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE I 146 " --> pdb=" O ALA I 141 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA I 141 " --> pdb=" O ILE I 146 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA I 148 " --> pdb=" O VAL I 139 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL I 139 " --> pdb=" O ALA I 148 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N THR I 150 " --> pdb=" O GLY I 137 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY I 137 " --> pdb=" O THR I 150 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR I 152 " --> pdb=" O LYS I 135 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS I 135 " --> pdb=" O TYR I 152 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU I 154 " --> pdb=" O ASN I 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN I 133 " --> pdb=" O LEU I 154 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL I 134 " --> pdb=" O ASN A 209 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER I 136 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR A 207 " --> pdb=" O SER I 136 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL A 204 " --> pdb=" O ALA A 188 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 13 through 14 removed outlier: 5.867A pdb=" N ILE I 171 " --> pdb=" O ASN I 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN I 165 " --> pdb=" O ILE I 171 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER I 173 " --> pdb=" O VAL I 163 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE I 146 " --> pdb=" O ALA I 141 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA I 141 " --> pdb=" O ILE I 146 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA I 148 " --> pdb=" O VAL I 139 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL I 139 " --> pdb=" O ALA I 148 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N THR I 150 " --> pdb=" O GLY I 137 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY I 137 " --> pdb=" O THR I 150 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR I 152 " --> pdb=" O LYS I 135 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS I 135 " --> pdb=" O TYR I 152 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU I 154 " --> pdb=" O ASN I 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN I 133 " --> pdb=" O LEU I 154 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL I 134 " --> pdb=" O ASN A 209 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER I 136 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR A 207 " --> pdb=" O SER I 136 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL A 204 " --> pdb=" O ALA A 188 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ILE A 171 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN A 165 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER A 173 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN A 42 " --> pdb=" O GLY A 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 13 through 14 removed outlier: 5.867A pdb=" N ILE I 171 " --> pdb=" O ASN I 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN I 165 " --> pdb=" O ILE I 171 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER I 173 " --> pdb=" O VAL I 163 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE I 146 " --> pdb=" O ALA I 141 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA I 141 " --> pdb=" O ILE I 146 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA I 148 " --> pdb=" O VAL I 139 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL I 139 " --> pdb=" O ALA I 148 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N THR I 150 " --> pdb=" O GLY I 137 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY I 137 " --> pdb=" O THR I 150 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR I 152 " --> pdb=" O LYS I 135 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS I 135 " --> pdb=" O TYR I 152 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU I 154 " --> pdb=" O ASN I 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN I 133 " --> pdb=" O LEU I 154 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL I 134 " --> pdb=" O ASN A 209 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER I 136 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR A 207 " --> pdb=" O SER I 136 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL A 204 " --> pdb=" O ALA A 188 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ILE A 171 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN A 165 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER A 173 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE A 146 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA A 141 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA A 148 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL A 139 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR A 150 " --> pdb=" O GLY A 137 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY A 137 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR A 152 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS A 135 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU A 154 " --> pdb=" O ASN A 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN A 133 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL A 134 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A 136 " --> pdb=" O THR B 207 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR B 207 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL B 204 " --> pdb=" O ALA B 188 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 13 through 14 removed outlier: 5.867A pdb=" N ILE I 171 " --> pdb=" O ASN I 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN I 165 " --> pdb=" O ILE I 171 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER I 173 " --> pdb=" O VAL I 163 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE I 146 " --> pdb=" O ALA I 141 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA I 141 " --> pdb=" O ILE I 146 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA I 148 " --> pdb=" O VAL I 139 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL I 139 " --> pdb=" O ALA I 148 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N THR I 150 " --> pdb=" O GLY I 137 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY I 137 " --> pdb=" O THR I 150 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR I 152 " --> pdb=" O LYS I 135 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS I 135 " --> pdb=" O TYR I 152 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU I 154 " --> pdb=" O ASN I 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN I 133 " --> pdb=" O LEU I 154 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL I 134 " --> pdb=" O ASN A 209 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER I 136 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR A 207 " --> pdb=" O SER I 136 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL A 204 " --> pdb=" O ALA A 188 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ILE A 171 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN A 165 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER A 173 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE A 146 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA A 141 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA A 148 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL A 139 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR A 150 " --> pdb=" O GLY A 137 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY A 137 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR A 152 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS A 135 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU A 154 " --> pdb=" O ASN A 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN A 133 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL A 134 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A 136 " --> pdb=" O THR B 207 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR B 207 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL B 204 " --> pdb=" O ALA B 188 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ILE B 171 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN B 165 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER B 173 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN B 42 " --> pdb=" O GLY B 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 13 through 14 removed outlier: 5.867A pdb=" N ILE I 171 " --> pdb=" O ASN I 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN I 165 " --> pdb=" O ILE I 171 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER I 173 " --> pdb=" O VAL I 163 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE I 146 " --> pdb=" O ALA I 141 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA I 141 " --> pdb=" O ILE I 146 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA I 148 " --> pdb=" O VAL I 139 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL I 139 " --> pdb=" O ALA I 148 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N THR I 150 " --> pdb=" O GLY I 137 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY I 137 " --> pdb=" O THR I 150 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR I 152 " --> pdb=" O LYS I 135 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS I 135 " --> pdb=" O TYR I 152 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU I 154 " --> pdb=" O ASN I 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN I 133 " --> pdb=" O LEU I 154 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL I 134 " --> pdb=" O ASN A 209 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER I 136 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR A 207 " --> pdb=" O SER I 136 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL A 204 " --> pdb=" O ALA A 188 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ILE A 171 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN A 165 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER A 173 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE A 146 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA A 141 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA A 148 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL A 139 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR A 150 " --> pdb=" O GLY A 137 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY A 137 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR A 152 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS A 135 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU A 154 " --> pdb=" O ASN A 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN A 133 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL A 134 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A 136 " --> pdb=" O THR B 207 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR B 207 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL B 204 " --> pdb=" O ALA B 188 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ILE B 171 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN B 165 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER B 173 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE B 146 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA B 141 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ALA B 148 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL B 139 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR B 150 " --> pdb=" O GLY B 137 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY B 137 " --> pdb=" O THR B 150 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR B 152 " --> pdb=" O LYS B 135 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS B 135 " --> pdb=" O TYR B 152 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU B 154 " --> pdb=" O ASN B 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN B 133 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL B 134 " --> pdb=" O ASN C 209 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER B 136 " --> pdb=" O THR C 207 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR C 207 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL C 204 " --> pdb=" O ALA C 188 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 13 through 14 removed outlier: 5.867A pdb=" N ILE I 171 " --> pdb=" O ASN I 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN I 165 " --> pdb=" O ILE I 171 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER I 173 " --> pdb=" O VAL I 163 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE I 146 " --> pdb=" O ALA I 141 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA I 141 " --> pdb=" O ILE I 146 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA I 148 " --> pdb=" O VAL I 139 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL I 139 " --> pdb=" O ALA I 148 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N THR I 150 " --> pdb=" O GLY I 137 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY I 137 " --> pdb=" O THR I 150 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR I 152 " --> pdb=" O LYS I 135 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS I 135 " --> pdb=" O TYR I 152 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU I 154 " --> pdb=" O ASN I 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN I 133 " --> pdb=" O LEU I 154 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL I 134 " --> pdb=" O ASN A 209 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER I 136 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR A 207 " --> pdb=" O SER I 136 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL A 204 " --> pdb=" O ALA A 188 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ILE A 171 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN A 165 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER A 173 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE A 146 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA A 141 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA A 148 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL A 139 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR A 150 " --> pdb=" O GLY A 137 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY A 137 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR A 152 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS A 135 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU A 154 " --> pdb=" O ASN A 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN A 133 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL A 134 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A 136 " --> pdb=" O THR B 207 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR B 207 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL B 204 " --> pdb=" O ALA B 188 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ILE B 171 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN B 165 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER B 173 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE B 146 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA B 141 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ALA B 148 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL B 139 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR B 150 " --> pdb=" O GLY B 137 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY B 137 " --> pdb=" O THR B 150 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR B 152 " --> pdb=" O LYS B 135 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS B 135 " --> pdb=" O TYR B 152 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU B 154 " --> pdb=" O ASN B 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN B 133 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL B 134 " --> pdb=" O ASN C 209 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER B 136 " --> pdb=" O THR C 207 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR C 207 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL C 204 " --> pdb=" O ALA C 188 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ILE C 171 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN C 165 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER C 173 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN C 42 " --> pdb=" O GLY C 125 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 13 through 14 removed outlier: 5.867A pdb=" N ILE I 171 " --> pdb=" O ASN I 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN I 165 " --> pdb=" O ILE I 171 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER I 173 " --> pdb=" O VAL I 163 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE I 146 " --> pdb=" O ALA I 141 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA I 141 " --> pdb=" O ILE I 146 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA I 148 " --> pdb=" O VAL I 139 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL I 139 " --> pdb=" O ALA I 148 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N THR I 150 " --> pdb=" O GLY I 137 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY I 137 " --> pdb=" O THR I 150 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR I 152 " --> pdb=" O LYS I 135 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS I 135 " --> pdb=" O TYR I 152 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU I 154 " --> pdb=" O ASN I 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN I 133 " --> pdb=" O LEU I 154 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL I 134 " --> pdb=" O ASN A 209 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER I 136 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR A 207 " --> pdb=" O SER I 136 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL A 204 " --> pdb=" O ALA A 188 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ILE A 171 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN A 165 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER A 173 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE A 146 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA A 141 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA A 148 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL A 139 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR A 150 " --> pdb=" O GLY A 137 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY A 137 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR A 152 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS A 135 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU A 154 " --> pdb=" O ASN A 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN A 133 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL A 134 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A 136 " --> pdb=" O THR B 207 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR B 207 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL B 204 " --> pdb=" O ALA B 188 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ILE B 171 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN B 165 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER B 173 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE B 146 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA B 141 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ALA B 148 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL B 139 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR B 150 " --> pdb=" O GLY B 137 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY B 137 " --> pdb=" O THR B 150 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR B 152 " --> pdb=" O LYS B 135 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS B 135 " --> pdb=" O TYR B 152 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU B 154 " --> pdb=" O ASN B 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN B 133 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL B 134 " --> pdb=" O ASN C 209 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER B 136 " --> pdb=" O THR C 207 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR C 207 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL C 204 " --> pdb=" O ALA C 188 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ILE C 171 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN C 165 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER C 173 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE C 146 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA C 141 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ALA C 148 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL C 139 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR C 150 " --> pdb=" O GLY C 137 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY C 137 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR C 152 " --> pdb=" O LYS C 135 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS C 135 " --> pdb=" O TYR C 152 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU C 154 " --> pdb=" O ASN C 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN C 133 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL C 134 " --> pdb=" O ASN D 209 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER C 136 " --> pdb=" O THR D 207 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR D 207 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL D 204 " --> pdb=" O ALA D 188 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 13 through 14 removed outlier: 5.867A pdb=" N ILE I 171 " --> pdb=" O ASN I 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN I 165 " --> pdb=" O ILE I 171 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER I 173 " --> pdb=" O VAL I 163 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE I 146 " --> pdb=" O ALA I 141 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA I 141 " --> pdb=" O ILE I 146 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA I 148 " --> pdb=" O VAL I 139 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL I 139 " --> pdb=" O ALA I 148 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N THR I 150 " --> pdb=" O GLY I 137 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY I 137 " --> pdb=" O THR I 150 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR I 152 " --> pdb=" O LYS I 135 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS I 135 " --> pdb=" O TYR I 152 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU I 154 " --> pdb=" O ASN I 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN I 133 " --> pdb=" O LEU I 154 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL I 134 " --> pdb=" O ASN A 209 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER I 136 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR A 207 " --> pdb=" O SER I 136 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL A 204 " --> pdb=" O ALA A 188 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ILE A 171 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN A 165 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER A 173 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE A 146 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA A 141 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA A 148 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL A 139 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR A 150 " --> pdb=" O GLY A 137 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY A 137 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR A 152 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS A 135 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU A 154 " --> pdb=" O ASN A 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN A 133 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL A 134 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A 136 " --> pdb=" O THR B 207 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR B 207 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL B 204 " --> pdb=" O ALA B 188 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ILE B 171 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN B 165 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER B 173 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE B 146 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA B 141 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ALA B 148 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL B 139 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR B 150 " --> pdb=" O GLY B 137 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY B 137 " --> pdb=" O THR B 150 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR B 152 " --> pdb=" O LYS B 135 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS B 135 " --> pdb=" O TYR B 152 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU B 154 " --> pdb=" O ASN B 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN B 133 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL B 134 " --> pdb=" O ASN C 209 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER B 136 " --> pdb=" O THR C 207 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR C 207 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL C 204 " --> pdb=" O ALA C 188 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ILE C 171 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN C 165 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER C 173 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE C 146 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA C 141 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ALA C 148 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL C 139 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR C 150 " --> pdb=" O GLY C 137 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY C 137 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR C 152 " --> pdb=" O LYS C 135 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS C 135 " --> pdb=" O TYR C 152 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU C 154 " --> pdb=" O ASN C 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN C 133 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL C 134 " --> pdb=" O ASN D 209 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER C 136 " --> pdb=" O THR D 207 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR D 207 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL D 204 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ILE D 171 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN D 165 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER D 173 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN D 42 " --> pdb=" O GLY D 125 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 13 through 14 removed outlier: 5.867A pdb=" N ILE I 171 " --> pdb=" O ASN I 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN I 165 " --> pdb=" O ILE I 171 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER I 173 " --> pdb=" O VAL I 163 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE I 146 " --> pdb=" O ALA I 141 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA I 141 " --> pdb=" O ILE I 146 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA I 148 " --> pdb=" O VAL I 139 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL I 139 " --> pdb=" O ALA I 148 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N THR I 150 " --> pdb=" O GLY I 137 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY I 137 " --> pdb=" O THR I 150 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR I 152 " --> pdb=" O LYS I 135 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS I 135 " --> pdb=" O TYR I 152 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU I 154 " --> pdb=" O ASN I 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN I 133 " --> pdb=" O LEU I 154 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL I 134 " --> pdb=" O ASN A 209 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER I 136 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR A 207 " --> pdb=" O SER I 136 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL A 204 " --> pdb=" O ALA A 188 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ILE A 171 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN A 165 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER A 173 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE A 146 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA A 141 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA A 148 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL A 139 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR A 150 " --> pdb=" O GLY A 137 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY A 137 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR A 152 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS A 135 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU A 154 " --> pdb=" O ASN A 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN A 133 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL A 134 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A 136 " --> pdb=" O THR B 207 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR B 207 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL B 204 " --> pdb=" O ALA B 188 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ILE B 171 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN B 165 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER B 173 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE B 146 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA B 141 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ALA B 148 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL B 139 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR B 150 " --> pdb=" O GLY B 137 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY B 137 " --> pdb=" O THR B 150 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR B 152 " --> pdb=" O LYS B 135 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS B 135 " --> pdb=" O TYR B 152 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU B 154 " --> pdb=" O ASN B 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN B 133 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL B 134 " --> pdb=" O ASN C 209 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER B 136 " --> pdb=" O THR C 207 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR C 207 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL C 204 " --> pdb=" O ALA C 188 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ILE C 171 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN C 165 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER C 173 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE C 146 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA C 141 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ALA C 148 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL C 139 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR C 150 " --> pdb=" O GLY C 137 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY C 137 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR C 152 " --> pdb=" O LYS C 135 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS C 135 " --> pdb=" O TYR C 152 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU C 154 " --> pdb=" O ASN C 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN C 133 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL C 134 " --> pdb=" O ASN D 209 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER C 136 " --> pdb=" O THR D 207 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR D 207 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL D 204 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ILE D 171 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN D 165 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER D 173 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE D 146 " --> pdb=" O ALA D 141 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA D 141 " --> pdb=" O ILE D 146 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA D 148 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL D 139 " --> pdb=" O ALA D 148 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR D 150 " --> pdb=" O GLY D 137 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLY D 137 " --> pdb=" O THR D 150 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR D 152 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS D 135 " --> pdb=" O TYR D 152 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU D 154 " --> pdb=" O ASN D 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN D 133 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL D 134 " --> pdb=" O ASN E 209 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER D 136 " --> pdb=" O THR E 207 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR E 207 " --> pdb=" O SER D 136 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL E 204 " --> pdb=" O ALA E 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 13 through 14 removed outlier: 5.867A pdb=" N ILE I 171 " --> pdb=" O ASN I 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN I 165 " --> pdb=" O ILE I 171 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER I 173 " --> pdb=" O VAL I 163 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE I 146 " --> pdb=" O ALA I 141 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA I 141 " --> pdb=" O ILE I 146 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA I 148 " --> pdb=" O VAL I 139 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL I 139 " --> pdb=" O ALA I 148 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N THR I 150 " --> pdb=" O GLY I 137 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY I 137 " --> pdb=" O THR I 150 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR I 152 " --> pdb=" O LYS I 135 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS I 135 " --> pdb=" O TYR I 152 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU I 154 " --> pdb=" O ASN I 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN I 133 " --> pdb=" O LEU I 154 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL I 134 " --> pdb=" O ASN A 209 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER I 136 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR A 207 " --> pdb=" O SER I 136 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL A 204 " --> pdb=" O ALA A 188 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ILE A 171 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN A 165 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER A 173 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE A 146 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA A 141 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA A 148 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL A 139 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR A 150 " --> pdb=" O GLY A 137 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY A 137 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR A 152 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS A 135 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU A 154 " --> pdb=" O ASN A 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN A 133 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL A 134 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A 136 " --> pdb=" O THR B 207 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR B 207 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL B 204 " --> pdb=" O ALA B 188 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ILE B 171 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN B 165 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER B 173 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE B 146 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA B 141 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ALA B 148 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL B 139 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR B 150 " --> pdb=" O GLY B 137 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY B 137 " --> pdb=" O THR B 150 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR B 152 " --> pdb=" O LYS B 135 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS B 135 " --> pdb=" O TYR B 152 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU B 154 " --> pdb=" O ASN B 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN B 133 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL B 134 " --> pdb=" O ASN C 209 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER B 136 " --> pdb=" O THR C 207 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR C 207 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL C 204 " --> pdb=" O ALA C 188 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ILE C 171 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN C 165 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER C 173 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE C 146 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA C 141 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ALA C 148 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL C 139 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR C 150 " --> pdb=" O GLY C 137 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY C 137 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR C 152 " --> pdb=" O LYS C 135 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS C 135 " --> pdb=" O TYR C 152 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU C 154 " --> pdb=" O ASN C 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN C 133 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL C 134 " --> pdb=" O ASN D 209 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER C 136 " --> pdb=" O THR D 207 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR D 207 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL D 204 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ILE D 171 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN D 165 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER D 173 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE D 146 " --> pdb=" O ALA D 141 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA D 141 " --> pdb=" O ILE D 146 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA D 148 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL D 139 " --> pdb=" O ALA D 148 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR D 150 " --> pdb=" O GLY D 137 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLY D 137 " --> pdb=" O THR D 150 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR D 152 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS D 135 " --> pdb=" O TYR D 152 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU D 154 " --> pdb=" O ASN D 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN D 133 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL D 134 " --> pdb=" O ASN E 209 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER D 136 " --> pdb=" O THR E 207 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR E 207 " --> pdb=" O SER D 136 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL E 204 " --> pdb=" O ALA E 188 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ILE E 171 " --> pdb=" O ASN E 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN E 165 " --> pdb=" O ILE E 171 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER E 173 " --> pdb=" O VAL E 163 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN E 42 " --> pdb=" O GLY E 125 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 13 through 14 removed outlier: 5.867A pdb=" N ILE F 171 " --> pdb=" O ASN F 165 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ASN F 165 " --> pdb=" O ILE F 171 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER F 173 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE F 146 " --> pdb=" O ALA F 141 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA F 141 " --> pdb=" O ILE F 146 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA F 148 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL F 139 " --> pdb=" O ALA F 148 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR F 150 " --> pdb=" O GLY F 137 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY F 137 " --> pdb=" O THR F 150 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR F 152 " --> pdb=" O LYS F 135 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS F 135 " --> pdb=" O TYR F 152 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU F 154 " --> pdb=" O ASN F 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN F 133 " --> pdb=" O LEU F 154 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL F 134 " --> pdb=" O ASN G 209 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER F 136 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N THR G 207 " --> pdb=" O SER F 136 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL G 204 " --> pdb=" O ALA G 188 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ILE G 171 " --> pdb=" O ASN G 165 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ASN G 165 " --> pdb=" O ILE G 171 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER G 173 " --> pdb=" O VAL G 163 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE G 146 " --> pdb=" O ALA G 141 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA G 141 " --> pdb=" O ILE G 146 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA G 148 " --> pdb=" O VAL G 139 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL G 139 " --> pdb=" O ALA G 148 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR G 150 " --> pdb=" O GLY G 137 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLY G 137 " --> pdb=" O THR G 150 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR G 152 " --> pdb=" O LYS G 135 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS G 135 " --> pdb=" O TYR G 152 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU G 154 " --> pdb=" O ASN G 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN G 133 " --> pdb=" O LEU G 154 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N VAL G 134 " --> pdb=" O ASN H 209 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR H 207 " --> pdb=" O SER G 136 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL H 204 " --> pdb=" O ALA H 188 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ILE H 171 " --> pdb=" O ASN H 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN H 165 " --> pdb=" O ILE H 171 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER H 173 " --> pdb=" O VAL H 163 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN H 42 " --> pdb=" O GLY H 125 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 41 through 42 removed outlier: 3.698A pdb=" N GLN F 42 " --> pdb=" O GLY F 125 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE F 146 " --> pdb=" O ALA F 141 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA F 141 " --> pdb=" O ILE F 146 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA F 148 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL F 139 " --> pdb=" O ALA F 148 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR F 150 " --> pdb=" O GLY F 137 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY F 137 " --> pdb=" O THR F 150 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR F 152 " --> pdb=" O LYS F 135 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS F 135 " --> pdb=" O TYR F 152 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU F 154 " --> pdb=" O ASN F 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN F 133 " --> pdb=" O LEU F 154 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL F 134 " --> pdb=" O ASN G 209 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER F 136 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N THR G 207 " --> pdb=" O SER F 136 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL G 204 " --> pdb=" O ALA G 188 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ILE G 171 " --> pdb=" O ASN G 165 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ASN G 165 " --> pdb=" O ILE G 171 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER G 173 " --> pdb=" O VAL G 163 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE G 146 " --> pdb=" O ALA G 141 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA G 141 " --> pdb=" O ILE G 146 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA G 148 " --> pdb=" O VAL G 139 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL G 139 " --> pdb=" O ALA G 148 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR G 150 " --> pdb=" O GLY G 137 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLY G 137 " --> pdb=" O THR G 150 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR G 152 " --> pdb=" O LYS G 135 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS G 135 " --> pdb=" O TYR G 152 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU G 154 " --> pdb=" O ASN G 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN G 133 " --> pdb=" O LEU G 154 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N VAL G 134 " --> pdb=" O ASN H 209 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR H 207 " --> pdb=" O SER G 136 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL H 204 " --> pdb=" O ALA H 188 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ILE H 171 " --> pdb=" O ASN H 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN H 165 " --> pdb=" O ILE H 171 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER H 173 " --> pdb=" O VAL H 163 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN H 42 " --> pdb=" O GLY H 125 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 13 through 14 removed outlier: 5.867A pdb=" N ILE G 171 " --> pdb=" O ASN G 165 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ASN G 165 " --> pdb=" O ILE G 171 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER G 173 " --> pdb=" O VAL G 163 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE G 146 " --> pdb=" O ALA G 141 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA G 141 " --> pdb=" O ILE G 146 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA G 148 " --> pdb=" O VAL G 139 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL G 139 " --> pdb=" O ALA G 148 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR G 150 " --> pdb=" O GLY G 137 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLY G 137 " --> pdb=" O THR G 150 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR G 152 " --> pdb=" O LYS G 135 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS G 135 " --> pdb=" O TYR G 152 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU G 154 " --> pdb=" O ASN G 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN G 133 " --> pdb=" O LEU G 154 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N VAL G 134 " --> pdb=" O ASN H 209 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR H 207 " --> pdb=" O SER G 136 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL H 204 " --> pdb=" O ALA H 188 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ILE H 171 " --> pdb=" O ASN H 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN H 165 " --> pdb=" O ILE H 171 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER H 173 " --> pdb=" O VAL H 163 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN H 42 " --> pdb=" O GLY H 125 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 41 through 42 removed outlier: 3.698A pdb=" N GLN G 42 " --> pdb=" O GLY G 125 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE G 146 " --> pdb=" O ALA G 141 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA G 141 " --> pdb=" O ILE G 146 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA G 148 " --> pdb=" O VAL G 139 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL G 139 " --> pdb=" O ALA G 148 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR G 150 " --> pdb=" O GLY G 137 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLY G 137 " --> pdb=" O THR G 150 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR G 152 " --> pdb=" O LYS G 135 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS G 135 " --> pdb=" O TYR G 152 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU G 154 " --> pdb=" O ASN G 133 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN G 133 " --> pdb=" O LEU G 154 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N VAL G 134 " --> pdb=" O ASN H 209 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR H 207 " --> pdb=" O SER G 136 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL H 204 " --> pdb=" O ALA H 188 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ILE H 171 " --> pdb=" O ASN H 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN H 165 " --> pdb=" O ILE H 171 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER H 173 " --> pdb=" O VAL H 163 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN H 42 " --> pdb=" O GLY H 125 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 13 through 14 removed outlier: 5.866A pdb=" N ILE H 171 " --> pdb=" O ASN H 165 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASN H 165 " --> pdb=" O ILE H 171 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER H 173 " --> pdb=" O VAL H 163 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN H 42 " --> pdb=" O GLY H 125 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 34 through 37 removed outlier: 6.340A pdb=" N ILE A 34 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LEU A 81 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL A 36 " --> pdb=" O LEU A 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 34 through 37 removed outlier: 6.340A pdb=" N ILE B 34 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LEU B 81 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL B 36 " --> pdb=" O LEU B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 34 through 37 removed outlier: 6.340A pdb=" N ILE C 34 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU C 81 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL C 36 " --> pdb=" O LEU C 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'D' and resid 34 through 37 removed outlier: 6.341A pdb=" N ILE D 34 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU D 81 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL D 36 " --> pdb=" O LEU D 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'E' and resid 34 through 37 removed outlier: 6.340A pdb=" N ILE E 34 " --> pdb=" O ILE E 79 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LEU E 81 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL E 36 " --> pdb=" O LEU E 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'F' and resid 34 through 37 removed outlier: 6.340A pdb=" N ILE F 34 " --> pdb=" O ILE F 79 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LEU F 81 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL F 36 " --> pdb=" O LEU F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'G' and resid 34 through 37 removed outlier: 6.340A pdb=" N ILE G 34 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU G 81 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL G 36 " --> pdb=" O LEU G 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'H' and resid 34 through 37 removed outlier: 6.340A pdb=" N ILE H 34 " --> pdb=" O ILE H 79 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LEU H 81 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL H 36 " --> pdb=" O LEU H 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'I' and resid 34 through 37 removed outlier: 6.340A pdb=" N ILE I 34 " --> pdb=" O ILE I 79 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LEU I 81 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL I 36 " --> pdb=" O LEU I 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 2279 hydrogen bonds defined for protein. 6585 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.06 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6555 1.34 - 1.45: 2668 1.45 - 1.57: 10712 1.57 - 1.69: 0 1.69 - 1.80: 135 Bond restraints: 20070 Sorted by residual: bond pdb=" N ASP C 195 " pdb=" CA ASP C 195 " ideal model delta sigma weight residual 1.457 1.497 -0.041 1.32e-02 5.74e+03 9.45e+00 bond pdb=" N ASP I 195 " pdb=" CA ASP I 195 " ideal model delta sigma weight residual 1.457 1.496 -0.040 1.32e-02 5.74e+03 9.02e+00 bond pdb=" N ASP D 195 " pdb=" CA ASP D 195 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.32e-02 5.74e+03 8.95e+00 bond pdb=" N ASP E 195 " pdb=" CA ASP E 195 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.32e-02 5.74e+03 8.95e+00 bond pdb=" N ASP H 195 " pdb=" CA ASP H 195 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.32e-02 5.74e+03 8.94e+00 ... (remaining 20065 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 26524 2.13 - 4.26: 624 4.26 - 6.39: 41 6.39 - 8.52: 9 8.52 - 10.65: 18 Bond angle restraints: 27216 Sorted by residual: angle pdb=" C ILE E 194 " pdb=" N ASP E 195 " pdb=" CA ASP E 195 " ideal model delta sigma weight residual 121.31 131.40 -10.09 1.49e+00 4.50e-01 4.59e+01 angle pdb=" C ILE F 194 " pdb=" N ASP F 195 " pdb=" CA ASP F 195 " ideal model delta sigma weight residual 121.31 131.40 -10.09 1.49e+00 4.50e-01 4.58e+01 angle pdb=" C ILE G 194 " pdb=" N ASP G 195 " pdb=" CA ASP G 195 " ideal model delta sigma weight residual 121.31 131.39 -10.08 1.49e+00 4.50e-01 4.58e+01 angle pdb=" C ILE A 194 " pdb=" N ASP A 195 " pdb=" CA ASP A 195 " ideal model delta sigma weight residual 121.31 131.39 -10.08 1.49e+00 4.50e-01 4.57e+01 angle pdb=" C ILE B 194 " pdb=" N ASP B 195 " pdb=" CA ASP B 195 " ideal model delta sigma weight residual 121.31 131.38 -10.07 1.49e+00 4.50e-01 4.57e+01 ... (remaining 27211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.24: 10606 15.24 - 30.48: 1121 30.48 - 45.71: 261 45.71 - 60.95: 72 60.95 - 76.19: 54 Dihedral angle restraints: 12114 sinusoidal: 4824 harmonic: 7290 Sorted by residual: dihedral pdb=" CA ASP F 195 " pdb=" C ASP F 195 " pdb=" N TYR F 196 " pdb=" CA TYR F 196 " ideal model delta harmonic sigma weight residual -180.00 -145.23 -34.77 0 5.00e+00 4.00e-02 4.84e+01 dihedral pdb=" CA ASP C 195 " pdb=" C ASP C 195 " pdb=" N TYR C 196 " pdb=" CA TYR C 196 " ideal model delta harmonic sigma weight residual -180.00 -145.24 -34.76 0 5.00e+00 4.00e-02 4.83e+01 dihedral pdb=" CA ASP D 195 " pdb=" C ASP D 195 " pdb=" N TYR D 196 " pdb=" CA TYR D 196 " ideal model delta harmonic sigma weight residual -180.00 -145.24 -34.76 0 5.00e+00 4.00e-02 4.83e+01 ... (remaining 12111 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1816 0.036 - 0.072: 853 0.072 - 0.108: 216 0.108 - 0.144: 136 0.144 - 0.179: 30 Chirality restraints: 3051 Sorted by residual: chirality pdb=" CA VAL H 139 " pdb=" N VAL H 139 " pdb=" C VAL H 139 " pdb=" CB VAL H 139 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.04e-01 chirality pdb=" CA VAL F 139 " pdb=" N VAL F 139 " pdb=" C VAL F 139 " pdb=" CB VAL F 139 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.93e-01 chirality pdb=" CA VAL D 139 " pdb=" N VAL D 139 " pdb=" C VAL D 139 " pdb=" CB VAL D 139 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.91e-01 ... (remaining 3048 not shown) Planarity restraints: 3591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN O 15 " 0.036 5.00e-02 4.00e+02 5.47e-02 4.78e+00 pdb=" N PRO O 16 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO O 16 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO O 16 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN M 15 " -0.036 5.00e-02 4.00e+02 5.46e-02 4.77e+00 pdb=" N PRO M 16 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO M 16 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO M 16 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 15 " 0.036 5.00e-02 4.00e+02 5.45e-02 4.75e+00 pdb=" N PRO R 16 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO R 16 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO R 16 " 0.030 5.00e-02 4.00e+02 ... (remaining 3588 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.90: 7510 2.90 - 3.40: 17287 3.40 - 3.90: 31109 3.90 - 4.40: 34729 4.40 - 4.90: 63947 Nonbonded interactions: 154582 Sorted by model distance: nonbonded pdb=" O GLN I 197 " pdb=" NH1 ARG I 198 " model vdw 2.395 3.120 nonbonded pdb=" O GLN D 197 " pdb=" NH1 ARG D 198 " model vdw 2.395 3.120 nonbonded pdb=" O GLN A 197 " pdb=" NH1 ARG A 198 " model vdw 2.395 3.120 nonbonded pdb=" O GLN G 197 " pdb=" NH1 ARG G 198 " model vdw 2.395 3.120 nonbonded pdb=" O GLN F 197 " pdb=" NH1 ARG F 198 " model vdw 2.395 3.120 ... (remaining 154577 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.170 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 20070 Z= 0.258 Angle : 0.836 10.647 27216 Z= 0.485 Chirality : 0.050 0.179 3051 Planarity : 0.006 0.055 3591 Dihedral : 14.700 76.188 7434 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.42 % Allowed : 7.95 % Favored : 91.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.38 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.67 (0.14), residues: 2484 helix: -4.68 (0.06), residues: 738 sheet: -2.08 (0.18), residues: 720 loop : -2.35 (0.17), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 93 TYR 0.014 0.002 TYR G 196 PHE 0.012 0.002 PHE G 144 TRP 0.004 0.001 TRP H 77 HIS 0.001 0.000 HIS B 26 Details of bonding type rmsd covalent geometry : bond 0.00543 (20070) covalent geometry : angle 0.83619 (27216) hydrogen bonds : bond 0.29398 ( 802) hydrogen bonds : angle 10.54361 ( 6585) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 400 time to evaluate : 0.764 Fit side-chains REVERT: A 11 ARG cc_start: 0.7611 (ptm-80) cc_final: 0.6806 (mmt90) REVERT: A 60 VAL cc_start: 0.9036 (t) cc_final: 0.8810 (m) REVERT: A 74 ASP cc_start: 0.7624 (m-30) cc_final: 0.7357 (m-30) REVERT: A 131 GLU cc_start: 0.7789 (tp30) cc_final: 0.7519 (tp30) REVERT: A 135 LYS cc_start: 0.8595 (mttt) cc_final: 0.8251 (mtpp) REVERT: B 11 ARG cc_start: 0.7838 (ptm-80) cc_final: 0.6991 (tpp-160) REVERT: B 22 LYS cc_start: 0.8891 (ttmt) cc_final: 0.8473 (mttm) REVERT: B 41 ILE cc_start: 0.9150 (mp) cc_final: 0.8799 (mt) REVERT: B 131 GLU cc_start: 0.7725 (tp30) cc_final: 0.7503 (tp30) REVERT: B 135 LYS cc_start: 0.8603 (mttt) cc_final: 0.8280 (mtpp) REVERT: B 239 LEU cc_start: 0.9171 (mt) cc_final: 0.8636 (mt) REVERT: C 22 LYS cc_start: 0.8875 (ttmt) cc_final: 0.8565 (ttpp) REVERT: C 49 LYS cc_start: 0.8816 (mttt) cc_final: 0.8613 (mttm) REVERT: C 135 LYS cc_start: 0.8548 (mttt) cc_final: 0.8321 (mttm) REVERT: C 239 LEU cc_start: 0.9008 (mt) cc_final: 0.8534 (mt) REVERT: D 23 ASP cc_start: 0.8030 (t0) cc_final: 0.7769 (t0) REVERT: D 131 GLU cc_start: 0.7722 (tp30) cc_final: 0.7400 (tp30) REVERT: D 135 LYS cc_start: 0.8522 (mttt) cc_final: 0.8182 (mttm) REVERT: D 210 GLU cc_start: 0.8406 (tt0) cc_final: 0.8139 (tt0) REVERT: D 239 LEU cc_start: 0.9142 (mt) cc_final: 0.8668 (mt) REVERT: D 256 MET cc_start: 0.8324 (mtm) cc_final: 0.8027 (mtp) REVERT: E 11 ARG cc_start: 0.7699 (ptm-80) cc_final: 0.6982 (mmt90) REVERT: E 22 LYS cc_start: 0.8936 (ttmt) cc_final: 0.8539 (mttm) REVERT: E 84 GLN cc_start: 0.8322 (tt0) cc_final: 0.8063 (tt0) REVERT: E 143 TYR cc_start: 0.8587 (t80) cc_final: 0.8219 (t80) REVERT: E 217 MET cc_start: 0.8023 (tpt) cc_final: 0.7790 (tpt) REVERT: E 239 LEU cc_start: 0.9152 (mt) cc_final: 0.8705 (mp) REVERT: F 11 ARG cc_start: 0.7667 (ptm-80) cc_final: 0.7019 (mmt-90) REVERT: F 22 LYS cc_start: 0.8704 (ttmt) cc_final: 0.8217 (mttm) REVERT: F 135 LYS cc_start: 0.8421 (mttt) cc_final: 0.8187 (mtmt) REVERT: F 143 TYR cc_start: 0.8568 (t80) cc_final: 0.8303 (t80) REVERT: F 239 LEU cc_start: 0.9143 (mt) cc_final: 0.8492 (mt) REVERT: G 22 LYS cc_start: 0.8830 (ttmt) cc_final: 0.8306 (mttm) REVERT: G 33 LYS cc_start: 0.8972 (mttt) cc_final: 0.8757 (mttm) REVERT: G 84 GLN cc_start: 0.8350 (tt0) cc_final: 0.8098 (tt0) REVERT: G 135 LYS cc_start: 0.8557 (mttt) cc_final: 0.8259 (mttm) REVERT: G 143 TYR cc_start: 0.8708 (t80) cc_final: 0.8306 (t80) REVERT: H 11 ARG cc_start: 0.7667 (ptm-80) cc_final: 0.6995 (mmt90) REVERT: H 22 LYS cc_start: 0.8597 (ttmt) cc_final: 0.8336 (mttm) REVERT: H 74 ASP cc_start: 0.7399 (m-30) cc_final: 0.7164 (m-30) REVERT: H 135 LYS cc_start: 0.8410 (mttt) cc_final: 0.8135 (mttm) REVERT: H 239 LEU cc_start: 0.9098 (mt) cc_final: 0.8639 (mp) REVERT: I 11 ARG cc_start: 0.7895 (ptm-80) cc_final: 0.6908 (mmt90) REVERT: I 22 LYS cc_start: 0.9049 (ttmt) cc_final: 0.8540 (mttm) REVERT: I 33 LYS cc_start: 0.9008 (mttt) cc_final: 0.8668 (mtpt) REVERT: I 39 TYR cc_start: 0.8644 (m-80) cc_final: 0.8424 (m-80) REVERT: I 60 VAL cc_start: 0.9104 (t) cc_final: 0.8867 (m) REVERT: I 131 GLU cc_start: 0.7611 (tp30) cc_final: 0.7326 (tp30) REVERT: I 135 LYS cc_start: 0.8550 (mttt) cc_final: 0.8270 (mtmm) REVERT: I 214 LEU cc_start: 0.8766 (tp) cc_final: 0.8512 (mt) REVERT: I 239 LEU cc_start: 0.9090 (mt) cc_final: 0.8847 (mp) REVERT: K 6 GLN cc_start: 0.8256 (mt0) cc_final: 0.7982 (mt0) REVERT: M 6 GLN cc_start: 0.8163 (mt0) cc_final: 0.7888 (mt0) REVERT: N 24 ASN cc_start: 0.9139 (m-40) cc_final: 0.8476 (m-40) REVERT: O 6 GLN cc_start: 0.8284 (mt0) cc_final: 0.8050 (mt0) REVERT: Q 6 GLN cc_start: 0.8103 (mt0) cc_final: 0.7893 (mt0) REVERT: Q 24 ASN cc_start: 0.9151 (m-40) cc_final: 0.8655 (m-40) REVERT: R 24 ASN cc_start: 0.9179 (m-40) cc_final: 0.8712 (m-40) outliers start: 9 outliers final: 9 residues processed: 408 average time/residue: 0.1670 time to fit residues: 99.8350 Evaluate side-chains 305 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 296 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain I residue 115 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN B 91 ASN C 91 ASN D 91 ASN E 91 ASN F 55 ASN F 91 ASN F 114 GLN G 91 ASN H 91 ASN I 91 ASN ** J 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 11 ASN ** N 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 11 ASN ** O 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 11 ASN ** Q 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.134479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.104746 restraints weight = 23119.435| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.28 r_work: 0.2966 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 20070 Z= 0.267 Angle : 0.680 8.107 27216 Z= 0.363 Chirality : 0.046 0.164 3051 Planarity : 0.005 0.036 3591 Dihedral : 4.963 23.534 2745 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.53 % Allowed : 14.04 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.08 (0.15), residues: 2484 helix: -2.78 (0.12), residues: 756 sheet: -1.55 (0.19), residues: 648 loop : -1.59 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 234 TYR 0.015 0.001 TYR A 184 PHE 0.015 0.002 PHE B 48 TRP 0.004 0.001 TRP C 77 HIS 0.001 0.000 HIS I 255 Details of bonding type rmsd covalent geometry : bond 0.00605 (20070) covalent geometry : angle 0.67956 (27216) hydrogen bonds : bond 0.04637 ( 802) hydrogen bonds : angle 3.59874 ( 6585) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 365 time to evaluate : 0.781 Fit side-chains REVERT: A 11 ARG cc_start: 0.8269 (ptm-80) cc_final: 0.6704 (mmt90) REVERT: A 22 LYS cc_start: 0.8856 (ttmt) cc_final: 0.8187 (mttm) REVERT: A 60 VAL cc_start: 0.9224 (t) cc_final: 0.8997 (m) REVERT: A 74 ASP cc_start: 0.8025 (m-30) cc_final: 0.7716 (m-30) REVERT: A 131 GLU cc_start: 0.8362 (tp30) cc_final: 0.7960 (tp30) REVERT: A 210 GLU cc_start: 0.8926 (tt0) cc_final: 0.8522 (tt0) REVERT: A 244 GLU cc_start: 0.8832 (tt0) cc_final: 0.8501 (tt0) REVERT: B 11 ARG cc_start: 0.8367 (ptm-80) cc_final: 0.7018 (mmt90) REVERT: B 41 ILE cc_start: 0.9153 (mp) cc_final: 0.8876 (mt) REVERT: B 42 GLN cc_start: 0.8387 (pt0) cc_final: 0.8065 (pt0) REVERT: C 11 ARG cc_start: 0.8436 (ptm-80) cc_final: 0.6859 (mmt90) REVERT: C 22 LYS cc_start: 0.9149 (ttmt) cc_final: 0.8797 (ttpp) REVERT: C 23 ASP cc_start: 0.8638 (t0) cc_final: 0.8346 (t0) REVERT: C 42 GLN cc_start: 0.8425 (pt0) cc_final: 0.8133 (pt0) REVERT: C 49 LYS cc_start: 0.8868 (mttt) cc_final: 0.8643 (mttm) REVERT: C 74 ASP cc_start: 0.7896 (m-30) cc_final: 0.7649 (m-30) REVERT: C 135 LYS cc_start: 0.8740 (mttt) cc_final: 0.8472 (mtmm) REVERT: D 22 LYS cc_start: 0.8961 (ttpt) cc_final: 0.8153 (mttm) REVERT: D 23 ASP cc_start: 0.8642 (t0) cc_final: 0.8383 (t0) REVERT: D 42 GLN cc_start: 0.8533 (pt0) cc_final: 0.8120 (pt0) REVERT: D 84 GLN cc_start: 0.8387 (tt0) cc_final: 0.8170 (tt0) REVERT: D 124 GLU cc_start: 0.8352 (pp20) cc_final: 0.7686 (tt0) REVERT: D 131 GLU cc_start: 0.8433 (tp30) cc_final: 0.8028 (tp30) REVERT: D 256 MET cc_start: 0.8371 (mtm) cc_final: 0.7794 (mtp) REVERT: E 11 ARG cc_start: 0.8039 (ptm-80) cc_final: 0.6788 (mmt90) REVERT: E 22 LYS cc_start: 0.9035 (ttmt) cc_final: 0.8164 (mttm) REVERT: E 84 GLN cc_start: 0.8565 (tt0) cc_final: 0.8365 (tt0) REVERT: E 124 GLU cc_start: 0.8247 (pp20) cc_final: 0.7704 (tt0) REVERT: E 131 GLU cc_start: 0.8362 (tp30) cc_final: 0.7941 (tp30) REVERT: E 213 MET cc_start: 0.8937 (ttp) cc_final: 0.8520 (ptm) REVERT: E 230 ASP cc_start: 0.8232 (t0) cc_final: 0.8022 (t0) REVERT: E 256 MET cc_start: 0.8246 (mtp) cc_final: 0.7817 (mtp) REVERT: F 11 ARG cc_start: 0.8176 (ptm-80) cc_final: 0.6690 (mmt90) REVERT: F 22 LYS cc_start: 0.8860 (ttmt) cc_final: 0.8100 (mttm) REVERT: F 60 VAL cc_start: 0.9175 (t) cc_final: 0.8940 (m) REVERT: F 124 GLU cc_start: 0.8195 (pp20) cc_final: 0.7719 (tt0) REVERT: F 135 LYS cc_start: 0.8716 (mttt) cc_final: 0.8412 (mtmm) REVERT: F 239 LEU cc_start: 0.8845 (mt) cc_final: 0.8620 (mt) REVERT: G 22 LYS cc_start: 0.8931 (ttmt) cc_final: 0.8274 (ptpp) REVERT: G 33 LYS cc_start: 0.9175 (mttt) cc_final: 0.8962 (mttm) REVERT: G 42 GLN cc_start: 0.8087 (pt0) cc_final: 0.7786 (pt0) REVERT: G 73 LYS cc_start: 0.8317 (tptt) cc_final: 0.7981 (tppt) REVERT: G 124 GLU cc_start: 0.8323 (pp20) cc_final: 0.7838 (tt0) REVERT: G 131 GLU cc_start: 0.8148 (tp30) cc_final: 0.7891 (tp30) REVERT: G 135 LYS cc_start: 0.8711 (mttt) cc_final: 0.8460 (mtpt) REVERT: G 244 GLU cc_start: 0.8772 (tt0) cc_final: 0.8528 (mt-10) REVERT: H 11 ARG cc_start: 0.8199 (ptm-80) cc_final: 0.6785 (mmt90) REVERT: H 22 LYS cc_start: 0.8817 (ttmt) cc_final: 0.8137 (ptpp) REVERT: H 135 LYS cc_start: 0.8643 (mttt) cc_final: 0.8381 (mttm) REVERT: H 217 MET cc_start: 0.8015 (tpt) cc_final: 0.7730 (tpp) REVERT: H 236 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8532 (mm) REVERT: I 11 ARG cc_start: 0.8199 (ptm-80) cc_final: 0.6660 (mmt90) REVERT: I 22 LYS cc_start: 0.9142 (ttmt) cc_final: 0.8366 (mttm) REVERT: I 33 LYS cc_start: 0.9247 (mttt) cc_final: 0.9007 (mtpt) REVERT: I 42 GLN cc_start: 0.8304 (pt0) cc_final: 0.8012 (pt0) REVERT: I 60 VAL cc_start: 0.9190 (t) cc_final: 0.8978 (m) REVERT: I 131 GLU cc_start: 0.8356 (tp30) cc_final: 0.7830 (tp30) REVERT: I 214 LEU cc_start: 0.8457 (tp) cc_final: 0.8147 (mp) REVERT: J 27 GLN cc_start: 0.8507 (mt0) cc_final: 0.8214 (mm-40) REVERT: K 6 GLN cc_start: 0.8735 (mt0) cc_final: 0.8375 (mt0) REVERT: K 27 GLN cc_start: 0.8887 (mt0) cc_final: 0.8624 (mt0) REVERT: L 6 GLN cc_start: 0.8578 (mt0) cc_final: 0.8272 (mt0) REVERT: M 6 GLN cc_start: 0.8679 (mt0) cc_final: 0.8382 (mt0) REVERT: O 6 GLN cc_start: 0.8628 (mt0) cc_final: 0.8245 (mt0) outliers start: 33 outliers final: 18 residues processed: 385 average time/residue: 0.1456 time to fit residues: 84.7397 Evaluate side-chains 334 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 315 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 185 GLU Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 31 SER Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain R residue 31 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 240 optimal weight: 1.9990 chunk 169 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 197 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 229 optimal weight: 0.9990 chunk 204 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 106 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 11 ASN ** R 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.139149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.109918 restraints weight = 22759.153| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.28 r_work: 0.3037 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 20070 Z= 0.128 Angle : 0.549 6.488 27216 Z= 0.292 Chirality : 0.043 0.157 3051 Planarity : 0.004 0.033 3591 Dihedral : 4.455 28.214 2736 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.49 % Allowed : 16.78 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.16), residues: 2484 helix: -1.04 (0.17), residues: 756 sheet: -0.81 (0.19), residues: 729 loop : -1.44 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 234 TYR 0.011 0.001 TYR A 184 PHE 0.009 0.001 PHE L 5 TRP 0.004 0.001 TRP D 77 HIS 0.001 0.000 HIS I 255 Details of bonding type rmsd covalent geometry : bond 0.00285 (20070) covalent geometry : angle 0.54943 (27216) hydrogen bonds : bond 0.03571 ( 802) hydrogen bonds : angle 2.85163 ( 6585) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 354 time to evaluate : 0.584 Fit side-chains REVERT: A 60 VAL cc_start: 0.9164 (t) cc_final: 0.8896 (m) REVERT: A 74 ASP cc_start: 0.7917 (m-30) cc_final: 0.7552 (m-30) REVERT: A 131 GLU cc_start: 0.8353 (tp30) cc_final: 0.7951 (tp30) REVERT: A 210 GLU cc_start: 0.8889 (tt0) cc_final: 0.8576 (tt0) REVERT: A 244 GLU cc_start: 0.8908 (tt0) cc_final: 0.8467 (tt0) REVERT: B 22 LYS cc_start: 0.8991 (ttpt) cc_final: 0.8736 (ttpp) REVERT: B 41 ILE cc_start: 0.9200 (mp) cc_final: 0.8825 (mt) REVERT: B 42 GLN cc_start: 0.8257 (pt0) cc_final: 0.8039 (pt0) REVERT: B 73 LYS cc_start: 0.8347 (tppt) cc_final: 0.7905 (tptp) REVERT: B 239 LEU cc_start: 0.8792 (mt) cc_final: 0.8502 (mt) REVERT: B 256 MET cc_start: 0.8224 (mtp) cc_final: 0.7906 (mtt) REVERT: C 22 LYS cc_start: 0.9142 (ttmt) cc_final: 0.8388 (mttm) REVERT: C 23 ASP cc_start: 0.8556 (t0) cc_final: 0.8355 (t0) REVERT: C 42 GLN cc_start: 0.8357 (pt0) cc_final: 0.8122 (pt0) REVERT: C 49 LYS cc_start: 0.8812 (mttt) cc_final: 0.8566 (mttm) REVERT: C 74 ASP cc_start: 0.8031 (m-30) cc_final: 0.7780 (m-30) REVERT: C 135 LYS cc_start: 0.8663 (mttt) cc_final: 0.8362 (mtmm) REVERT: C 210 GLU cc_start: 0.8336 (tt0) cc_final: 0.8118 (tt0) REVERT: D 22 LYS cc_start: 0.8882 (ttpt) cc_final: 0.8220 (mttm) REVERT: D 42 GLN cc_start: 0.8482 (pt0) cc_final: 0.7916 (pt0) REVERT: D 74 ASP cc_start: 0.7886 (m-30) cc_final: 0.7354 (m-30) REVERT: D 94 LYS cc_start: 0.8659 (mtmm) cc_final: 0.8443 (mtmt) REVERT: D 124 GLU cc_start: 0.8295 (pp20) cc_final: 0.7603 (tt0) REVERT: D 131 GLU cc_start: 0.8382 (tp30) cc_final: 0.7778 (tp30) REVERT: D 143 TYR cc_start: 0.8951 (t80) cc_final: 0.8695 (t80) REVERT: D 210 GLU cc_start: 0.8457 (tt0) cc_final: 0.8092 (tt0) REVERT: D 256 MET cc_start: 0.8079 (mtm) cc_final: 0.7784 (mtp) REVERT: E 22 LYS cc_start: 0.9001 (ttmt) cc_final: 0.8656 (ttpp) REVERT: E 33 LYS cc_start: 0.9280 (mttt) cc_final: 0.8960 (mttm) REVERT: E 42 GLN cc_start: 0.8199 (pt0) cc_final: 0.7972 (pt0) REVERT: E 124 GLU cc_start: 0.8184 (pp20) cc_final: 0.7740 (pp20) REVERT: E 131 GLU cc_start: 0.8359 (tp30) cc_final: 0.7932 (tp30) REVERT: E 230 ASP cc_start: 0.8288 (t0) cc_final: 0.8057 (m-30) REVERT: E 244 GLU cc_start: 0.8773 (tt0) cc_final: 0.8476 (tt0) REVERT: F 22 LYS cc_start: 0.8821 (ttmt) cc_final: 0.8076 (mttm) REVERT: F 124 GLU cc_start: 0.8061 (pp20) cc_final: 0.7717 (pp20) REVERT: F 135 LYS cc_start: 0.8615 (mttt) cc_final: 0.8348 (mtmm) REVERT: F 244 GLU cc_start: 0.8759 (tt0) cc_final: 0.8533 (tt0) REVERT: F 256 MET cc_start: 0.8084 (mtp) cc_final: 0.7764 (mtt) REVERT: G 22 LYS cc_start: 0.8920 (ttmt) cc_final: 0.8328 (ptpp) REVERT: G 42 GLN cc_start: 0.7874 (pt0) cc_final: 0.7624 (pt0) REVERT: G 73 LYS cc_start: 0.8181 (tptt) cc_final: 0.7927 (tppt) REVERT: G 135 LYS cc_start: 0.8611 (mttt) cc_final: 0.8369 (mtpt) REVERT: G 143 TYR cc_start: 0.9001 (t80) cc_final: 0.8789 (t80) REVERT: G 210 GLU cc_start: 0.8636 (tt0) cc_final: 0.8360 (tt0) REVERT: G 256 MET cc_start: 0.8196 (mtp) cc_final: 0.7555 (mtt) REVERT: H 11 ARG cc_start: 0.8113 (ptm-80) cc_final: 0.6779 (mmt90) REVERT: H 22 LYS cc_start: 0.8901 (ttmt) cc_final: 0.8286 (ptpp) REVERT: H 135 LYS cc_start: 0.8729 (mttt) cc_final: 0.8398 (mtpt) REVERT: H 236 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8410 (mm) REVERT: H 244 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8572 (tt0) REVERT: I 11 ARG cc_start: 0.8154 (ptm-80) cc_final: 0.6630 (mmt90) REVERT: I 22 LYS cc_start: 0.9044 (ttmt) cc_final: 0.8129 (mttm) REVERT: I 42 GLN cc_start: 0.8329 (pt0) cc_final: 0.8061 (pt0) REVERT: I 60 VAL cc_start: 0.9158 (t) cc_final: 0.8948 (m) REVERT: I 131 GLU cc_start: 0.8313 (tp30) cc_final: 0.7811 (tp30) REVERT: I 230 ASP cc_start: 0.8493 (t0) cc_final: 0.8024 (m-30) REVERT: J 27 GLN cc_start: 0.8354 (mt0) cc_final: 0.8137 (mm-40) REVERT: K 6 GLN cc_start: 0.8684 (mt0) cc_final: 0.8320 (mt0) REVERT: K 27 GLN cc_start: 0.8815 (mt0) cc_final: 0.8552 (mt0) REVERT: L 6 GLN cc_start: 0.8483 (mt0) cc_final: 0.8230 (mt0) REVERT: M 6 GLN cc_start: 0.8639 (mt0) cc_final: 0.8334 (mt0) REVERT: O 6 GLN cc_start: 0.8572 (mt0) cc_final: 0.8187 (mt0) outliers start: 32 outliers final: 17 residues processed: 381 average time/residue: 0.1354 time to fit residues: 79.0275 Evaluate side-chains 338 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 320 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 185 GLU Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain J residue 25 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 70 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 128 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 200 optimal weight: 0.6980 chunk 125 optimal weight: 3.9990 chunk 219 optimal weight: 0.0970 chunk 202 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN ** J 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.138155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.108832 restraints weight = 22740.674| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.28 r_work: 0.3009 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20070 Z= 0.147 Angle : 0.554 8.396 27216 Z= 0.290 Chirality : 0.044 0.156 3051 Planarity : 0.004 0.028 3591 Dihedral : 4.251 26.360 2736 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.37 % Allowed : 17.29 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.17), residues: 2484 helix: -0.03 (0.19), residues: 756 sheet: -0.48 (0.20), residues: 729 loop : -1.23 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 234 TYR 0.012 0.001 TYR D 253 PHE 0.014 0.001 PHE G 144 TRP 0.003 0.001 TRP D 237 HIS 0.001 0.000 HIS H 255 Details of bonding type rmsd covalent geometry : bond 0.00332 (20070) covalent geometry : angle 0.55383 (27216) hydrogen bonds : bond 0.03492 ( 802) hydrogen bonds : angle 2.73866 ( 6585) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 341 time to evaluate : 0.769 Fit side-chains revert: symmetry clash REVERT: A 60 VAL cc_start: 0.9143 (t) cc_final: 0.8865 (m) REVERT: A 74 ASP cc_start: 0.7926 (m-30) cc_final: 0.7213 (m-30) REVERT: A 131 GLU cc_start: 0.8340 (tp30) cc_final: 0.7993 (tp30) REVERT: A 135 LYS cc_start: 0.8745 (mttt) cc_final: 0.8530 (mtmm) REVERT: A 244 GLU cc_start: 0.8925 (tt0) cc_final: 0.8470 (tt0) REVERT: A 256 MET cc_start: 0.8352 (mtp) cc_final: 0.7856 (mtt) REVERT: B 22 LYS cc_start: 0.8937 (ttpt) cc_final: 0.8677 (ttpp) REVERT: B 41 ILE cc_start: 0.9194 (mp) cc_final: 0.8940 (mt) REVERT: B 42 GLN cc_start: 0.8361 (pt0) cc_final: 0.8072 (pt0) REVERT: B 74 ASP cc_start: 0.8124 (m-30) cc_final: 0.7757 (m-30) REVERT: B 124 GLU cc_start: 0.8339 (pp20) cc_final: 0.7975 (pp20) REVERT: C 22 LYS cc_start: 0.9143 (ttmt) cc_final: 0.8336 (mttm) REVERT: C 23 ASP cc_start: 0.8667 (t0) cc_final: 0.8454 (t0) REVERT: C 42 GLN cc_start: 0.8347 (pt0) cc_final: 0.8122 (pt0) REVERT: C 74 ASP cc_start: 0.7999 (m-30) cc_final: 0.7783 (m-30) REVERT: C 135 LYS cc_start: 0.8696 (mttt) cc_final: 0.8389 (mtmm) REVERT: C 210 GLU cc_start: 0.8248 (tt0) cc_final: 0.7942 (tt0) REVERT: D 22 LYS cc_start: 0.8882 (ttpt) cc_final: 0.8090 (mttm) REVERT: D 42 GLN cc_start: 0.8440 (pt0) cc_final: 0.7878 (pt0) REVERT: D 84 GLN cc_start: 0.8506 (tt0) cc_final: 0.7970 (mt0) REVERT: D 94 LYS cc_start: 0.8628 (mtmm) cc_final: 0.8407 (mtmt) REVERT: D 124 GLU cc_start: 0.8347 (pp20) cc_final: 0.7663 (tt0) REVERT: D 131 GLU cc_start: 0.8287 (tp30) cc_final: 0.7685 (tp30) REVERT: D 210 GLU cc_start: 0.8535 (tt0) cc_final: 0.8189 (tt0) REVERT: E 22 LYS cc_start: 0.8972 (ttmt) cc_final: 0.8658 (ttpp) REVERT: E 33 LYS cc_start: 0.9278 (mttt) cc_final: 0.8994 (mttm) REVERT: E 124 GLU cc_start: 0.8211 (pp20) cc_final: 0.7762 (pp20) REVERT: E 213 MET cc_start: 0.8847 (ptt) cc_final: 0.8491 (ptm) REVERT: E 230 ASP cc_start: 0.8460 (t0) cc_final: 0.8078 (m-30) REVERT: F 22 LYS cc_start: 0.8811 (ttmt) cc_final: 0.8056 (mttm) REVERT: F 124 GLU cc_start: 0.8127 (pp20) cc_final: 0.7687 (tt0) REVERT: F 135 LYS cc_start: 0.8608 (mttt) cc_final: 0.8398 (mtmm) REVERT: F 256 MET cc_start: 0.8133 (mtp) cc_final: 0.7842 (mtt) REVERT: G 42 GLN cc_start: 0.7885 (pt0) cc_final: 0.7560 (pt0) REVERT: G 135 LYS cc_start: 0.8568 (mttt) cc_final: 0.8314 (mtpt) REVERT: G 210 GLU cc_start: 0.8655 (tt0) cc_final: 0.8349 (tt0) REVERT: H 22 LYS cc_start: 0.8870 (ttmt) cc_final: 0.8261 (ptpp) REVERT: H 135 LYS cc_start: 0.8694 (mttt) cc_final: 0.8376 (mtpt) REVERT: H 236 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8364 (mm) REVERT: H 244 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8575 (tt0) REVERT: I 22 LYS cc_start: 0.9012 (ttmt) cc_final: 0.8100 (mttm) REVERT: I 42 GLN cc_start: 0.8356 (pt0) cc_final: 0.8074 (pt0) REVERT: I 60 VAL cc_start: 0.9125 (t) cc_final: 0.8902 (m) REVERT: I 131 GLU cc_start: 0.8286 (tp30) cc_final: 0.7844 (tp30) REVERT: I 230 ASP cc_start: 0.8480 (t0) cc_final: 0.8011 (m-30) REVERT: K 6 GLN cc_start: 0.8675 (mt0) cc_final: 0.8309 (mt0) REVERT: K 27 GLN cc_start: 0.8815 (mt0) cc_final: 0.8559 (mt0) REVERT: L 6 GLN cc_start: 0.8477 (mt0) cc_final: 0.8226 (mt0) REVERT: M 6 GLN cc_start: 0.8644 (mt0) cc_final: 0.8336 (mt0) REVERT: O 6 GLN cc_start: 0.8543 (mt0) cc_final: 0.8160 (mt0) outliers start: 51 outliers final: 33 residues processed: 379 average time/residue: 0.1387 time to fit residues: 80.7618 Evaluate side-chains 350 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 316 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 185 GLU Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain R residue 31 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 169 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 176 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 116 optimal weight: 0.8980 chunk 236 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 GLN ** J 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.143547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.117437 restraints weight = 22466.389| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.85 r_work: 0.3131 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20070 Z= 0.139 Angle : 0.537 7.748 27216 Z= 0.282 Chirality : 0.043 0.155 3051 Planarity : 0.003 0.027 3591 Dihedral : 4.162 26.791 2736 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.93 % Allowed : 17.11 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.18), residues: 2484 helix: 0.50 (0.19), residues: 756 sheet: -0.24 (0.20), residues: 729 loop : -1.06 (0.21), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 234 TYR 0.011 0.001 TYR D 253 PHE 0.012 0.001 PHE G 144 TRP 0.002 0.001 TRP D 77 HIS 0.001 0.000 HIS D 255 Details of bonding type rmsd covalent geometry : bond 0.00314 (20070) covalent geometry : angle 0.53725 (27216) hydrogen bonds : bond 0.03365 ( 802) hydrogen bonds : angle 2.64732 ( 6585) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 314 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: A 74 ASP cc_start: 0.7925 (m-30) cc_final: 0.7240 (m-30) REVERT: A 131 GLU cc_start: 0.8218 (tp30) cc_final: 0.7800 (tp30) REVERT: A 135 LYS cc_start: 0.8569 (mttt) cc_final: 0.8363 (mtmm) REVERT: A 244 GLU cc_start: 0.8901 (tt0) cc_final: 0.8443 (tt0) REVERT: B 22 LYS cc_start: 0.8903 (ttpt) cc_final: 0.8667 (ttpp) REVERT: B 41 ILE cc_start: 0.9120 (mp) cc_final: 0.8866 (mt) REVERT: B 42 GLN cc_start: 0.8318 (pt0) cc_final: 0.7991 (pt0) REVERT: B 124 GLU cc_start: 0.8328 (pp20) cc_final: 0.7875 (pp20) REVERT: B 198 ARG cc_start: 0.7878 (mmt-90) cc_final: 0.7450 (mmt-90) REVERT: C 22 LYS cc_start: 0.9092 (ttmt) cc_final: 0.8266 (mttm) REVERT: C 42 GLN cc_start: 0.8309 (pt0) cc_final: 0.8071 (pt0) REVERT: C 43 ASP cc_start: 0.7229 (t0) cc_final: 0.6910 (t0) REVERT: C 74 ASP cc_start: 0.8121 (m-30) cc_final: 0.7906 (m-30) REVERT: C 135 LYS cc_start: 0.8590 (mttt) cc_final: 0.8264 (mtmm) REVERT: C 210 GLU cc_start: 0.8153 (tt0) cc_final: 0.7818 (tt0) REVERT: D 22 LYS cc_start: 0.8764 (ttpt) cc_final: 0.8396 (ttpp) REVERT: D 42 GLN cc_start: 0.8372 (pt0) cc_final: 0.7774 (pt0) REVERT: D 74 ASP cc_start: 0.7795 (m-30) cc_final: 0.7276 (m-30) REVERT: D 84 GLN cc_start: 0.8529 (tt0) cc_final: 0.7970 (mt0) REVERT: D 124 GLU cc_start: 0.8309 (pp20) cc_final: 0.7672 (tt0) REVERT: D 131 GLU cc_start: 0.8138 (tp30) cc_final: 0.7585 (tp30) REVERT: D 143 TYR cc_start: 0.8867 (t80) cc_final: 0.8665 (t80) REVERT: D 210 GLU cc_start: 0.8451 (tt0) cc_final: 0.8095 (tt0) REVERT: E 22 LYS cc_start: 0.8881 (ttmt) cc_final: 0.8601 (ttpp) REVERT: E 33 LYS cc_start: 0.9275 (mttt) cc_final: 0.8969 (mttm) REVERT: E 124 GLU cc_start: 0.8099 (pp20) cc_final: 0.7660 (pp20) REVERT: E 230 ASP cc_start: 0.8387 (t0) cc_final: 0.8046 (m-30) REVERT: F 22 LYS cc_start: 0.8719 (ttmt) cc_final: 0.7968 (mttm) REVERT: F 124 GLU cc_start: 0.7941 (pp20) cc_final: 0.7614 (tt0) REVERT: F 135 LYS cc_start: 0.8497 (mttt) cc_final: 0.8274 (mtmm) REVERT: F 256 MET cc_start: 0.8153 (mtp) cc_final: 0.7869 (mtt) REVERT: G 124 GLU cc_start: 0.8185 (pp20) cc_final: 0.7864 (pp20) REVERT: G 131 GLU cc_start: 0.7968 (tp30) cc_final: 0.7646 (tp30) REVERT: G 217 MET cc_start: 0.8300 (tpp) cc_final: 0.8010 (tpp) REVERT: H 22 LYS cc_start: 0.8819 (ttmt) cc_final: 0.8221 (ptpp) REVERT: H 135 LYS cc_start: 0.8604 (mttt) cc_final: 0.8262 (mtpt) REVERT: H 166 VAL cc_start: 0.8631 (OUTLIER) cc_final: 0.8394 (p) REVERT: H 236 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8332 (mm) REVERT: I 22 LYS cc_start: 0.8968 (ttmt) cc_final: 0.8524 (ttpp) REVERT: I 42 GLN cc_start: 0.8317 (pt0) cc_final: 0.8024 (pt0) REVERT: I 60 VAL cc_start: 0.9079 (t) cc_final: 0.8848 (m) REVERT: I 131 GLU cc_start: 0.8183 (tp30) cc_final: 0.7724 (tp30) REVERT: I 230 ASP cc_start: 0.8468 (t0) cc_final: 0.7926 (m-30) REVERT: I 256 MET cc_start: 0.7697 (mtt) cc_final: 0.7447 (mtt) REVERT: K 6 GLN cc_start: 0.8657 (mt0) cc_final: 0.8284 (mt0) REVERT: K 27 GLN cc_start: 0.8758 (mt0) cc_final: 0.8493 (mt0) REVERT: L 6 GLN cc_start: 0.8422 (mt0) cc_final: 0.8142 (mt0) REVERT: M 6 GLN cc_start: 0.8578 (mt0) cc_final: 0.8267 (mt0) REVERT: O 6 GLN cc_start: 0.8541 (mt0) cc_final: 0.8173 (mt0) REVERT: P 3 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8617 (mmp) outliers start: 63 outliers final: 53 residues processed: 358 average time/residue: 0.1431 time to fit residues: 78.0086 Evaluate side-chains 358 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 302 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 185 GLU Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 183 SER Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain I residue 251 VAL Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain P residue 3 MET Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 31 SER Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain R residue 31 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 145 optimal weight: 0.8980 chunk 121 optimal weight: 0.5980 chunk 193 optimal weight: 0.8980 chunk 225 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 236 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 chunk 231 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 GLN ** J 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.143957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.117874 restraints weight = 22452.865| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.85 r_work: 0.3139 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20070 Z= 0.133 Angle : 0.525 7.829 27216 Z= 0.276 Chirality : 0.043 0.153 3051 Planarity : 0.003 0.026 3591 Dihedral : 4.065 26.081 2736 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.98 % Allowed : 18.18 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.18), residues: 2484 helix: 0.88 (0.20), residues: 756 sheet: -0.09 (0.20), residues: 729 loop : -0.94 (0.21), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 8 TYR 0.010 0.001 TYR D 253 PHE 0.011 0.001 PHE G 144 TRP 0.003 0.001 TRP F 237 HIS 0.001 0.000 HIS D 255 Details of bonding type rmsd covalent geometry : bond 0.00301 (20070) covalent geometry : angle 0.52530 (27216) hydrogen bonds : bond 0.03273 ( 802) hydrogen bonds : angle 2.59072 ( 6585) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 312 time to evaluate : 0.656 Fit side-chains revert: symmetry clash REVERT: A 74 ASP cc_start: 0.7988 (m-30) cc_final: 0.7358 (m-30) REVERT: A 131 GLU cc_start: 0.8208 (tp30) cc_final: 0.7776 (tp30) REVERT: A 135 LYS cc_start: 0.8521 (mttt) cc_final: 0.8306 (mtmm) REVERT: A 244 GLU cc_start: 0.8916 (tt0) cc_final: 0.8523 (tt0) REVERT: B 41 ILE cc_start: 0.9107 (mp) cc_final: 0.8858 (mt) REVERT: B 42 GLN cc_start: 0.8467 (pt0) cc_final: 0.8119 (pt0) REVERT: B 73 LYS cc_start: 0.8217 (tppt) cc_final: 0.7791 (tptp) REVERT: B 74 ASP cc_start: 0.8098 (m-30) cc_final: 0.7766 (m-30) REVERT: B 124 GLU cc_start: 0.8380 (pp20) cc_final: 0.7924 (pp20) REVERT: B 198 ARG cc_start: 0.7934 (mmt-90) cc_final: 0.7483 (mmt-90) REVERT: C 42 GLN cc_start: 0.8338 (pt0) cc_final: 0.8091 (pt0) REVERT: C 43 ASP cc_start: 0.7213 (t0) cc_final: 0.6892 (t0) REVERT: C 74 ASP cc_start: 0.8112 (m-30) cc_final: 0.7897 (m-30) REVERT: C 135 LYS cc_start: 0.8592 (mttt) cc_final: 0.8274 (mtmm) REVERT: C 198 ARG cc_start: 0.7996 (mmt-90) cc_final: 0.7647 (mmt180) REVERT: C 210 GLU cc_start: 0.8147 (tt0) cc_final: 0.7810 (tt0) REVERT: D 42 GLN cc_start: 0.8361 (pt0) cc_final: 0.7889 (pt0) REVERT: D 44 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7869 (mt-10) REVERT: D 74 ASP cc_start: 0.7876 (m-30) cc_final: 0.7344 (m-30) REVERT: D 84 GLN cc_start: 0.8520 (tt0) cc_final: 0.8022 (mt0) REVERT: D 124 GLU cc_start: 0.8307 (pp20) cc_final: 0.7668 (tt0) REVERT: D 131 GLU cc_start: 0.8136 (tp30) cc_final: 0.7534 (tp30) REVERT: D 210 GLU cc_start: 0.8380 (tt0) cc_final: 0.8087 (tt0) REVERT: E 22 LYS cc_start: 0.8866 (ttmt) cc_final: 0.8603 (ttpp) REVERT: E 33 LYS cc_start: 0.9271 (mttt) cc_final: 0.8956 (mttm) REVERT: E 124 GLU cc_start: 0.8088 (pp20) cc_final: 0.7635 (pp20) REVERT: E 198 ARG cc_start: 0.7860 (mmt-90) cc_final: 0.7521 (mmt180) REVERT: E 230 ASP cc_start: 0.8387 (t0) cc_final: 0.8034 (m-30) REVERT: F 22 LYS cc_start: 0.8804 (ttmt) cc_final: 0.8113 (mttm) REVERT: F 124 GLU cc_start: 0.7895 (pp20) cc_final: 0.7631 (tt0) REVERT: G 42 GLN cc_start: 0.7843 (pt0) cc_final: 0.7586 (pt0) REVERT: G 124 GLU cc_start: 0.8181 (pp20) cc_final: 0.7849 (pp20) REVERT: G 131 GLU cc_start: 0.7954 (tp30) cc_final: 0.7610 (tp30) REVERT: G 217 MET cc_start: 0.8341 (tpp) cc_final: 0.8016 (tpp) REVERT: H 135 LYS cc_start: 0.8500 (mttt) cc_final: 0.8149 (mtpt) REVERT: H 236 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8332 (mm) REVERT: I 22 LYS cc_start: 0.8906 (ttmt) cc_final: 0.8514 (ttpp) REVERT: I 42 GLN cc_start: 0.8352 (pt0) cc_final: 0.8050 (pt0) REVERT: I 60 VAL cc_start: 0.9072 (t) cc_final: 0.8838 (m) REVERT: I 131 GLU cc_start: 0.8176 (tp30) cc_final: 0.7675 (tp30) REVERT: I 230 ASP cc_start: 0.8484 (t0) cc_final: 0.7890 (m-30) REVERT: K 6 GLN cc_start: 0.8663 (mt0) cc_final: 0.8298 (mt0) REVERT: K 27 GLN cc_start: 0.8740 (mt0) cc_final: 0.8530 (mt0) REVERT: L 6 GLN cc_start: 0.8431 (mt0) cc_final: 0.8159 (mt0) REVERT: M 6 GLN cc_start: 0.8576 (mt0) cc_final: 0.8257 (mt0) REVERT: N 27 GLN cc_start: 0.8366 (mt0) cc_final: 0.8122 (tp40) REVERT: O 6 GLN cc_start: 0.8547 (mt0) cc_final: 0.8187 (mt0) outliers start: 64 outliers final: 55 residues processed: 357 average time/residue: 0.1406 time to fit residues: 76.3353 Evaluate side-chains 360 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 304 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 185 GLU Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 183 SER Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain I residue 251 VAL Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain R residue 31 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 104 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 236 optimal weight: 2.9990 chunk 125 optimal weight: 0.2980 chunk 1 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 171 optimal weight: 0.6980 chunk 226 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 144 optimal weight: 0.5980 chunk 197 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 GLN ** J 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.144767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.118772 restraints weight = 22529.456| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.85 r_work: 0.3153 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20070 Z= 0.123 Angle : 0.517 7.702 27216 Z= 0.271 Chirality : 0.043 0.152 3051 Planarity : 0.003 0.028 3591 Dihedral : 4.007 26.254 2736 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.74 % Allowed : 18.41 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.18), residues: 2484 helix: 1.21 (0.20), residues: 756 sheet: -0.02 (0.21), residues: 729 loop : -0.88 (0.21), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 8 TYR 0.009 0.001 TYR D 253 PHE 0.010 0.001 PHE G 144 TRP 0.003 0.001 TRP F 77 HIS 0.000 0.000 HIS I 255 Details of bonding type rmsd covalent geometry : bond 0.00277 (20070) covalent geometry : angle 0.51704 (27216) hydrogen bonds : bond 0.03167 ( 802) hydrogen bonds : angle 2.52465 ( 6585) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 314 time to evaluate : 0.619 Fit side-chains revert: symmetry clash REVERT: A 74 ASP cc_start: 0.7947 (m-30) cc_final: 0.7401 (m-30) REVERT: A 124 GLU cc_start: 0.8043 (pp20) cc_final: 0.7783 (pp20) REVERT: A 131 GLU cc_start: 0.8219 (tp30) cc_final: 0.7789 (tp30) REVERT: A 244 GLU cc_start: 0.8916 (tt0) cc_final: 0.8526 (tt0) REVERT: B 41 ILE cc_start: 0.9088 (mp) cc_final: 0.8843 (mt) REVERT: B 42 GLN cc_start: 0.8465 (pt0) cc_final: 0.8116 (pt0) REVERT: B 73 LYS cc_start: 0.8195 (tppt) cc_final: 0.7788 (tptp) REVERT: B 124 GLU cc_start: 0.8363 (pp20) cc_final: 0.7887 (pp20) REVERT: B 198 ARG cc_start: 0.7899 (mmt-90) cc_final: 0.7451 (mmt-90) REVERT: C 42 GLN cc_start: 0.8291 (pt0) cc_final: 0.8041 (pt0) REVERT: C 43 ASP cc_start: 0.7189 (t0) cc_final: 0.6863 (t0) REVERT: C 74 ASP cc_start: 0.8121 (m-30) cc_final: 0.7901 (m-30) REVERT: C 135 LYS cc_start: 0.8523 (mttt) cc_final: 0.8237 (mtmm) REVERT: C 198 ARG cc_start: 0.7984 (mmt-90) cc_final: 0.7628 (mmt180) REVERT: C 210 GLU cc_start: 0.8144 (tt0) cc_final: 0.7804 (tt0) REVERT: D 22 LYS cc_start: 0.8639 (ttmt) cc_final: 0.8233 (ttpp) REVERT: D 42 GLN cc_start: 0.8286 (pt0) cc_final: 0.7860 (pt0) REVERT: D 44 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7780 (mt-10) REVERT: D 74 ASP cc_start: 0.7869 (m-30) cc_final: 0.7315 (m-30) REVERT: D 84 GLN cc_start: 0.8582 (tt0) cc_final: 0.8033 (mt0) REVERT: D 124 GLU cc_start: 0.8287 (pp20) cc_final: 0.7662 (tt0) REVERT: D 131 GLU cc_start: 0.8131 (tp30) cc_final: 0.7541 (tp30) REVERT: D 210 GLU cc_start: 0.8372 (tt0) cc_final: 0.8074 (tt0) REVERT: E 22 LYS cc_start: 0.8902 (ttmt) cc_final: 0.8526 (ttpp) REVERT: E 124 GLU cc_start: 0.7993 (pp20) cc_final: 0.7629 (pp20) REVERT: E 198 ARG cc_start: 0.7822 (mmt-90) cc_final: 0.7495 (mmt180) REVERT: E 213 MET cc_start: 0.8723 (ptt) cc_final: 0.8320 (ptm) REVERT: E 230 ASP cc_start: 0.8383 (t0) cc_final: 0.8005 (m-30) REVERT: F 22 LYS cc_start: 0.8806 (ttmt) cc_final: 0.8109 (mttm) REVERT: F 124 GLU cc_start: 0.7969 (pp20) cc_final: 0.7683 (tt0) REVERT: F 256 MET cc_start: 0.8187 (mtp) cc_final: 0.7911 (mtt) REVERT: G 42 GLN cc_start: 0.7831 (pt0) cc_final: 0.7454 (pt0) REVERT: G 124 GLU cc_start: 0.8163 (pp20) cc_final: 0.7837 (pp20) REVERT: G 131 GLU cc_start: 0.7972 (tp30) cc_final: 0.7611 (tp30) REVERT: G 198 ARG cc_start: 0.8015 (mmt-90) cc_final: 0.7572 (mmp80) REVERT: G 213 MET cc_start: 0.8751 (ptt) cc_final: 0.8412 (ptm) REVERT: G 217 MET cc_start: 0.8341 (tpp) cc_final: 0.8006 (tpp) REVERT: H 135 LYS cc_start: 0.8493 (mttt) cc_final: 0.8149 (mtpt) REVERT: H 236 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8340 (mm) REVERT: I 22 LYS cc_start: 0.8929 (ttmt) cc_final: 0.8509 (ttpp) REVERT: I 42 GLN cc_start: 0.8344 (pt0) cc_final: 0.8056 (pt0) REVERT: I 124 GLU cc_start: 0.7772 (tt0) cc_final: 0.7467 (pt0) REVERT: I 131 GLU cc_start: 0.8182 (tp30) cc_final: 0.7680 (tp30) REVERT: I 230 ASP cc_start: 0.8488 (t0) cc_final: 0.7871 (m-30) REVERT: K 6 GLN cc_start: 0.8670 (mt0) cc_final: 0.8306 (mt0) REVERT: K 27 GLN cc_start: 0.8723 (mt0) cc_final: 0.8513 (mt0) REVERT: L 6 GLN cc_start: 0.8451 (mt0) cc_final: 0.8187 (mt0) REVERT: M 6 GLN cc_start: 0.8573 (mt0) cc_final: 0.8250 (mt0) REVERT: N 27 GLN cc_start: 0.8355 (mt0) cc_final: 0.8136 (tp40) REVERT: O 6 GLN cc_start: 0.8549 (mt0) cc_final: 0.8182 (mt0) outliers start: 59 outliers final: 51 residues processed: 358 average time/residue: 0.1513 time to fit residues: 82.2961 Evaluate side-chains 351 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 299 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 185 GLU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 183 SER Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain I residue 251 VAL Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain R residue 31 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 42 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 180 optimal weight: 0.8980 chunk 191 optimal weight: 0.0980 chunk 229 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 120 optimal weight: 0.0370 chunk 118 optimal weight: 2.9990 chunk 141 optimal weight: 0.7980 chunk 119 optimal weight: 0.8980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 GLN ** J 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.146322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.120510 restraints weight = 22436.912| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.85 r_work: 0.3176 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20070 Z= 0.099 Angle : 0.495 7.482 27216 Z= 0.260 Chirality : 0.042 0.149 3051 Planarity : 0.003 0.029 3591 Dihedral : 3.880 26.333 2736 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.46 % Allowed : 18.78 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.18), residues: 2484 helix: 1.41 (0.20), residues: 765 sheet: 0.07 (0.21), residues: 729 loop : -0.73 (0.21), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Q 8 TYR 0.014 0.001 TYR D 143 PHE 0.007 0.001 PHE G 144 TRP 0.002 0.000 TRP E 237 HIS 0.001 0.000 HIS E 26 Details of bonding type rmsd covalent geometry : bond 0.00222 (20070) covalent geometry : angle 0.49527 (27216) hydrogen bonds : bond 0.02980 ( 802) hydrogen bonds : angle 2.41483 ( 6585) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 321 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 ARG cc_start: 0.8072 (ptm-80) cc_final: 0.6532 (mmt90) REVERT: A 74 ASP cc_start: 0.7967 (m-30) cc_final: 0.7502 (m-30) REVERT: A 82 GLU cc_start: 0.8990 (tp30) cc_final: 0.8365 (tp30) REVERT: A 131 GLU cc_start: 0.8181 (tp30) cc_final: 0.7819 (tp30) REVERT: A 244 GLU cc_start: 0.8886 (tt0) cc_final: 0.8637 (tt0) REVERT: A 256 MET cc_start: 0.8138 (mtp) cc_final: 0.7748 (mtt) REVERT: B 41 ILE cc_start: 0.9044 (mp) cc_final: 0.8783 (mt) REVERT: B 42 GLN cc_start: 0.8456 (pt0) cc_final: 0.8077 (pt0) REVERT: B 73 LYS cc_start: 0.8183 (tppt) cc_final: 0.7799 (tptp) REVERT: B 124 GLU cc_start: 0.8345 (pp20) cc_final: 0.7877 (pp20) REVERT: B 198 ARG cc_start: 0.7823 (mmt-90) cc_final: 0.7411 (mmt-90) REVERT: C 42 GLN cc_start: 0.8123 (pt0) cc_final: 0.7863 (pt0) REVERT: C 43 ASP cc_start: 0.7113 (t0) cc_final: 0.6815 (t0) REVERT: C 74 ASP cc_start: 0.8091 (m-30) cc_final: 0.7878 (m-30) REVERT: C 135 LYS cc_start: 0.8525 (mttt) cc_final: 0.8162 (mtpt) REVERT: C 198 ARG cc_start: 0.7868 (mmt-90) cc_final: 0.7510 (mmp80) REVERT: C 210 GLU cc_start: 0.8122 (tt0) cc_final: 0.7779 (tt0) REVERT: C 244 GLU cc_start: 0.8624 (tt0) cc_final: 0.8156 (tp30) REVERT: D 22 LYS cc_start: 0.8637 (ttmt) cc_final: 0.8222 (ttpp) REVERT: D 42 GLN cc_start: 0.8272 (pt0) cc_final: 0.7875 (pt0) REVERT: D 44 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7770 (mt-10) REVERT: D 74 ASP cc_start: 0.7856 (m-30) cc_final: 0.7651 (m-30) REVERT: D 84 GLN cc_start: 0.8477 (tt0) cc_final: 0.8109 (mp-120) REVERT: D 122 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.8040 (ttp) REVERT: D 124 GLU cc_start: 0.8332 (pp20) cc_final: 0.7688 (tt0) REVERT: D 131 GLU cc_start: 0.8105 (tp30) cc_final: 0.7557 (tp30) REVERT: D 143 TYR cc_start: 0.8766 (t80) cc_final: 0.8550 (t80) REVERT: D 210 GLU cc_start: 0.8359 (tt0) cc_final: 0.8086 (tt0) REVERT: E 124 GLU cc_start: 0.7987 (pp20) cc_final: 0.7641 (pp20) REVERT: E 198 ARG cc_start: 0.7798 (mmt-90) cc_final: 0.7479 (mmt180) REVERT: E 213 MET cc_start: 0.8674 (ptt) cc_final: 0.8291 (ptm) REVERT: E 230 ASP cc_start: 0.8374 (t0) cc_final: 0.8020 (m-30) REVERT: F 22 LYS cc_start: 0.8803 (ttmt) cc_final: 0.8051 (mttm) REVERT: F 124 GLU cc_start: 0.7928 (pp20) cc_final: 0.7637 (tt0) REVERT: F 221 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7741 (mt-10) REVERT: F 256 MET cc_start: 0.8144 (mtp) cc_final: 0.7870 (mtt) REVERT: G 42 GLN cc_start: 0.7677 (pt0) cc_final: 0.7461 (pt0) REVERT: G 124 GLU cc_start: 0.8122 (pp20) cc_final: 0.7784 (pp20) REVERT: G 131 GLU cc_start: 0.7968 (tp30) cc_final: 0.7585 (tp30) REVERT: G 198 ARG cc_start: 0.7897 (mmt-90) cc_final: 0.7449 (mmp80) REVERT: G 213 MET cc_start: 0.8723 (ptt) cc_final: 0.8484 (ptm) REVERT: G 217 MET cc_start: 0.8264 (tpp) cc_final: 0.7926 (tpp) REVERT: G 256 MET cc_start: 0.8202 (mtp) cc_final: 0.7482 (mtt) REVERT: H 135 LYS cc_start: 0.8562 (mttt) cc_final: 0.8254 (mtpt) REVERT: H 236 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8344 (mm) REVERT: I 22 LYS cc_start: 0.8914 (ttmt) cc_final: 0.8533 (ttpp) REVERT: I 42 GLN cc_start: 0.8324 (pt0) cc_final: 0.8033 (pt0) REVERT: I 74 ASP cc_start: 0.7734 (m-30) cc_final: 0.7277 (m-30) REVERT: I 124 GLU cc_start: 0.7711 (tt0) cc_final: 0.7416 (pt0) REVERT: I 131 GLU cc_start: 0.8141 (tp30) cc_final: 0.7643 (tp30) REVERT: I 135 LYS cc_start: 0.8346 (mttt) cc_final: 0.7997 (mtmm) REVERT: I 230 ASP cc_start: 0.8484 (t0) cc_final: 0.7879 (m-30) REVERT: K 6 GLN cc_start: 0.8693 (mt0) cc_final: 0.8312 (mt0) REVERT: K 27 GLN cc_start: 0.8708 (mt0) cc_final: 0.8454 (mt0) REVERT: L 6 GLN cc_start: 0.8450 (mt0) cc_final: 0.8198 (mt0) REVERT: M 6 GLN cc_start: 0.8508 (mt0) cc_final: 0.8172 (mt0) REVERT: O 6 GLN cc_start: 0.8544 (mt0) cc_final: 0.8173 (mt0) REVERT: P 27 GLN cc_start: 0.8518 (mt0) cc_final: 0.8102 (tp40) outliers start: 53 outliers final: 41 residues processed: 359 average time/residue: 0.1583 time to fit residues: 85.2649 Evaluate side-chains 342 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 298 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 185 GLU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain F residue 221 GLU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 84 GLN Chi-restraints excluded: chain H residue 183 SER Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain I residue 251 VAL Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain R residue 31 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 103 optimal weight: 0.5980 chunk 145 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 217 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 204 optimal weight: 3.9990 chunk 219 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 198 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.144723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.118749 restraints weight = 22381.694| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.84 r_work: 0.3152 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20070 Z= 0.127 Angle : 0.522 7.528 27216 Z= 0.272 Chirality : 0.043 0.151 3051 Planarity : 0.003 0.031 3591 Dihedral : 3.886 25.830 2736 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.46 % Allowed : 18.83 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.18), residues: 2484 helix: 1.60 (0.20), residues: 756 sheet: 0.09 (0.21), residues: 729 loop : -0.72 (0.21), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Q 8 TYR 0.013 0.001 TYR A 253 PHE 0.011 0.001 PHE G 144 TRP 0.003 0.001 TRP I 237 HIS 0.001 0.000 HIS H 26 Details of bonding type rmsd covalent geometry : bond 0.00288 (20070) covalent geometry : angle 0.52206 (27216) hydrogen bonds : bond 0.03155 ( 802) hydrogen bonds : angle 2.49951 ( 6585) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 312 time to evaluate : 0.733 Fit side-chains revert: symmetry clash REVERT: A 11 ARG cc_start: 0.8091 (ptm-80) cc_final: 0.6540 (mmt90) REVERT: A 74 ASP cc_start: 0.7994 (m-30) cc_final: 0.7525 (m-30) REVERT: A 131 GLU cc_start: 0.8185 (tp30) cc_final: 0.7822 (tp30) REVERT: A 244 GLU cc_start: 0.8897 (tt0) cc_final: 0.8650 (tt0) REVERT: A 256 MET cc_start: 0.8155 (mtp) cc_final: 0.7782 (mtt) REVERT: B 42 GLN cc_start: 0.8480 (pt0) cc_final: 0.8229 (pt0) REVERT: B 73 LYS cc_start: 0.8156 (tppt) cc_final: 0.7813 (tptp) REVERT: B 82 GLU cc_start: 0.8956 (tp30) cc_final: 0.8750 (tp30) REVERT: B 84 GLN cc_start: 0.8289 (mt0) cc_final: 0.8072 (mp10) REVERT: B 124 GLU cc_start: 0.8314 (pp20) cc_final: 0.7866 (pp20) REVERT: B 198 ARG cc_start: 0.7914 (mmt-90) cc_final: 0.7468 (mmt-90) REVERT: C 42 GLN cc_start: 0.8185 (pt0) cc_final: 0.7898 (pt0) REVERT: C 43 ASP cc_start: 0.7130 (t0) cc_final: 0.6802 (t0) REVERT: C 74 ASP cc_start: 0.8103 (m-30) cc_final: 0.7863 (m-30) REVERT: C 135 LYS cc_start: 0.8523 (mttt) cc_final: 0.8155 (mtpt) REVERT: C 198 ARG cc_start: 0.7987 (mmt-90) cc_final: 0.7615 (mmt180) REVERT: C 210 GLU cc_start: 0.8141 (tt0) cc_final: 0.7788 (tt0) REVERT: C 244 GLU cc_start: 0.8596 (tt0) cc_final: 0.8211 (tp30) REVERT: D 22 LYS cc_start: 0.8692 (ttmt) cc_final: 0.8242 (ttpp) REVERT: D 42 GLN cc_start: 0.8303 (pt0) cc_final: 0.7849 (pt0) REVERT: D 44 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7711 (mt-10) REVERT: D 84 GLN cc_start: 0.8484 (tt0) cc_final: 0.8101 (mp-120) REVERT: D 124 GLU cc_start: 0.8322 (pp20) cc_final: 0.7684 (tt0) REVERT: D 131 GLU cc_start: 0.8190 (tp30) cc_final: 0.7605 (tp30) REVERT: D 210 GLU cc_start: 0.8381 (tt0) cc_final: 0.8075 (tt0) REVERT: E 124 GLU cc_start: 0.8011 (pp20) cc_final: 0.7646 (pp20) REVERT: E 198 ARG cc_start: 0.7911 (mmt-90) cc_final: 0.7581 (mmt180) REVERT: E 213 MET cc_start: 0.8703 (ptt) cc_final: 0.8327 (ptm) REVERT: E 230 ASP cc_start: 0.8409 (t0) cc_final: 0.8024 (m-30) REVERT: F 22 LYS cc_start: 0.8807 (ttmt) cc_final: 0.8105 (mttm) REVERT: F 124 GLU cc_start: 0.7951 (pp20) cc_final: 0.7706 (tt0) REVERT: F 221 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7811 (mt-10) REVERT: F 256 MET cc_start: 0.8178 (mtp) cc_final: 0.7898 (mtt) REVERT: G 42 GLN cc_start: 0.7744 (pt0) cc_final: 0.7388 (pt0) REVERT: G 124 GLU cc_start: 0.8149 (pp20) cc_final: 0.7831 (pp20) REVERT: G 131 GLU cc_start: 0.7982 (tp30) cc_final: 0.7597 (tp30) REVERT: G 198 ARG cc_start: 0.8055 (mmt-90) cc_final: 0.7634 (mmp80) REVERT: G 213 MET cc_start: 0.8750 (ptt) cc_final: 0.8492 (ptm) REVERT: G 217 MET cc_start: 0.8262 (tpp) cc_final: 0.7909 (tpp) REVERT: G 256 MET cc_start: 0.8189 (mtp) cc_final: 0.7436 (mtt) REVERT: H 135 LYS cc_start: 0.8466 (mttt) cc_final: 0.8155 (mtpt) REVERT: H 198 ARG cc_start: 0.7821 (mmt-90) cc_final: 0.6765 (mpt180) REVERT: H 236 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8341 (mm) REVERT: I 22 LYS cc_start: 0.8964 (ttmt) cc_final: 0.8531 (ttpp) REVERT: I 74 ASP cc_start: 0.7787 (m-30) cc_final: 0.7309 (m-30) REVERT: I 124 GLU cc_start: 0.7737 (tt0) cc_final: 0.7415 (pt0) REVERT: I 131 GLU cc_start: 0.8154 (tp30) cc_final: 0.7639 (tp30) REVERT: I 230 ASP cc_start: 0.8491 (t0) cc_final: 0.7864 (m-30) REVERT: I 256 MET cc_start: 0.7821 (mtt) cc_final: 0.7398 (mtt) REVERT: K 6 GLN cc_start: 0.8696 (mt0) cc_final: 0.8329 (mt0) REVERT: K 27 GLN cc_start: 0.8709 (mt0) cc_final: 0.8464 (mt0) REVERT: L 6 GLN cc_start: 0.8450 (mt0) cc_final: 0.8192 (mt0) REVERT: M 6 GLN cc_start: 0.8515 (mt0) cc_final: 0.8163 (mt0) REVERT: O 6 GLN cc_start: 0.8549 (mt0) cc_final: 0.8179 (mt0) outliers start: 53 outliers final: 47 residues processed: 353 average time/residue: 0.1531 time to fit residues: 82.4849 Evaluate side-chains 356 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 307 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 185 GLU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain F residue 221 GLU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 183 SER Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain I residue 251 VAL Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain R residue 31 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 8 optimal weight: 0.6980 chunk 178 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 148 optimal weight: 0.4980 chunk 115 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 202 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 GLN ** J 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.141817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.115987 restraints weight = 22442.715| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.81 r_work: 0.3118 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20070 Z= 0.176 Angle : 0.567 8.177 27216 Z= 0.295 Chirality : 0.044 0.157 3051 Planarity : 0.003 0.031 3591 Dihedral : 4.052 25.268 2736 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.74 % Allowed : 18.74 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.18), residues: 2484 helix: 1.55 (0.20), residues: 756 sheet: 0.05 (0.21), residues: 729 loop : -0.76 (0.21), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Q 8 TYR 0.018 0.001 TYR D 143 PHE 0.015 0.001 PHE G 144 TRP 0.005 0.001 TRP F 77 HIS 0.001 0.000 HIS F 26 Details of bonding type rmsd covalent geometry : bond 0.00404 (20070) covalent geometry : angle 0.56721 (27216) hydrogen bonds : bond 0.03451 ( 802) hydrogen bonds : angle 2.66819 ( 6585) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 322 time to evaluate : 0.733 Fit side-chains revert: symmetry clash REVERT: A 11 ARG cc_start: 0.8131 (ptm-80) cc_final: 0.6528 (mmt90) REVERT: A 74 ASP cc_start: 0.8033 (m-30) cc_final: 0.7475 (m-30) REVERT: A 124 GLU cc_start: 0.8132 (pp20) cc_final: 0.7686 (tt0) REVERT: A 131 GLU cc_start: 0.8179 (tp30) cc_final: 0.7741 (tp30) REVERT: A 244 GLU cc_start: 0.8883 (tt0) cc_final: 0.8647 (tt0) REVERT: B 22 LYS cc_start: 0.8933 (ttpt) cc_final: 0.8545 (ttpp) REVERT: B 42 GLN cc_start: 0.8542 (pt0) cc_final: 0.8241 (pt0) REVERT: B 73 LYS cc_start: 0.8180 (tppt) cc_final: 0.7790 (tptp) REVERT: B 82 GLU cc_start: 0.8938 (tp30) cc_final: 0.8728 (tp30) REVERT: B 124 GLU cc_start: 0.8318 (pp20) cc_final: 0.7947 (pp20) REVERT: B 198 ARG cc_start: 0.7983 (mmt-90) cc_final: 0.7712 (mmt-90) REVERT: C 43 ASP cc_start: 0.7237 (t0) cc_final: 0.6853 (t0) REVERT: C 74 ASP cc_start: 0.8144 (m-30) cc_final: 0.7901 (m-30) REVERT: C 135 LYS cc_start: 0.8505 (mttt) cc_final: 0.8248 (mtmm) REVERT: C 198 ARG cc_start: 0.8084 (mmt-90) cc_final: 0.7691 (mmt180) REVERT: C 210 GLU cc_start: 0.8171 (tt0) cc_final: 0.7807 (tt0) REVERT: D 22 LYS cc_start: 0.8700 (ttmt) cc_final: 0.8262 (ttpp) REVERT: D 42 GLN cc_start: 0.8335 (pt0) cc_final: 0.7952 (pt0) REVERT: D 44 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7731 (mt-10) REVERT: D 74 ASP cc_start: 0.7820 (m-30) cc_final: 0.7293 (m-30) REVERT: D 84 GLN cc_start: 0.8428 (tt0) cc_final: 0.8021 (mt0) REVERT: D 124 GLU cc_start: 0.8306 (pp20) cc_final: 0.7705 (tt0) REVERT: D 131 GLU cc_start: 0.8169 (tp30) cc_final: 0.7527 (tp30) REVERT: D 210 GLU cc_start: 0.8412 (tt0) cc_final: 0.8077 (tt0) REVERT: D 244 GLU cc_start: 0.8664 (tt0) cc_final: 0.7649 (tp30) REVERT: E 22 LYS cc_start: 0.8803 (ttmt) cc_final: 0.8322 (ttpp) REVERT: E 124 GLU cc_start: 0.8059 (pp20) cc_final: 0.7647 (pp20) REVERT: E 198 ARG cc_start: 0.7957 (mmt-90) cc_final: 0.7567 (mmt180) REVERT: E 213 MET cc_start: 0.8769 (ptt) cc_final: 0.8364 (ptm) REVERT: E 221 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8137 (mt-10) REVERT: E 230 ASP cc_start: 0.8382 (t0) cc_final: 0.7893 (m-30) REVERT: F 22 LYS cc_start: 0.8728 (ttmt) cc_final: 0.7990 (mttm) REVERT: F 221 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7821 (mt-10) REVERT: F 252 LYS cc_start: 0.8234 (ttpt) cc_final: 0.8005 (tttm) REVERT: G 42 GLN cc_start: 0.7843 (pt0) cc_final: 0.7591 (pt0) REVERT: G 73 LYS cc_start: 0.8088 (tptt) cc_final: 0.7783 (tptt) REVERT: G 124 GLU cc_start: 0.8157 (pp20) cc_final: 0.7844 (tt0) REVERT: G 198 ARG cc_start: 0.8191 (mmt-90) cc_final: 0.7697 (mmp80) REVERT: G 213 MET cc_start: 0.8853 (ptt) cc_final: 0.8502 (ptm) REVERT: G 217 MET cc_start: 0.8356 (tpp) cc_final: 0.7995 (tpp) REVERT: H 135 LYS cc_start: 0.8456 (mttt) cc_final: 0.8112 (mtpt) REVERT: H 236 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8344 (mm) REVERT: I 22 LYS cc_start: 0.8939 (ttmt) cc_final: 0.8015 (mttm) REVERT: I 60 VAL cc_start: 0.9068 (t) cc_final: 0.8832 (m) REVERT: I 74 ASP cc_start: 0.7826 (m-30) cc_final: 0.7361 (m-30) REVERT: I 131 GLU cc_start: 0.8187 (tp30) cc_final: 0.7621 (tp30) REVERT: I 230 ASP cc_start: 0.8498 (t0) cc_final: 0.7852 (m-30) REVERT: I 256 MET cc_start: 0.7803 (mtt) cc_final: 0.7454 (mtt) REVERT: K 6 GLN cc_start: 0.8662 (mt0) cc_final: 0.8295 (mt0) REVERT: K 27 GLN cc_start: 0.8733 (mt0) cc_final: 0.8527 (mt0) REVERT: L 6 GLN cc_start: 0.8450 (mt0) cc_final: 0.8188 (mt0) REVERT: M 6 GLN cc_start: 0.8570 (mt0) cc_final: 0.8226 (mt0) REVERT: O 6 GLN cc_start: 0.8564 (mt0) cc_final: 0.8245 (mt0) REVERT: O 22 LEU cc_start: 0.8718 (mt) cc_final: 0.8453 (mt) outliers start: 59 outliers final: 52 residues processed: 366 average time/residue: 0.1515 time to fit residues: 83.5042 Evaluate side-chains 361 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 307 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 185 GLU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain F residue 221 GLU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 183 SER Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain R residue 31 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 45 optimal weight: 0.7980 chunk 191 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 chunk 122 optimal weight: 0.5980 chunk 194 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 174 optimal weight: 0.6980 chunk 229 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 GLN I 84 GLN ** J 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.142707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.116925 restraints weight = 22569.011| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.83 r_work: 0.3130 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20070 Z= 0.152 Angle : 0.553 7.670 27216 Z= 0.288 Chirality : 0.044 0.155 3051 Planarity : 0.003 0.031 3591 Dihedral : 4.039 25.995 2736 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.74 % Allowed : 18.74 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.18), residues: 2484 helix: 1.62 (0.20), residues: 756 sheet: 0.07 (0.21), residues: 729 loop : -0.72 (0.21), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Q 8 TYR 0.014 0.001 TYR A 253 PHE 0.019 0.001 PHE H 144 TRP 0.004 0.001 TRP G 237 HIS 0.001 0.000 HIS G 26 Details of bonding type rmsd covalent geometry : bond 0.00349 (20070) covalent geometry : angle 0.55305 (27216) hydrogen bonds : bond 0.03308 ( 802) hydrogen bonds : angle 2.60321 ( 6585) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4390.88 seconds wall clock time: 75 minutes 57.45 seconds (4557.45 seconds total)